Yum, tasty mutations...

MutationTaster - study a chromosomal position

MTQE documentation
NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 4 transcript(s)...
Querying Taster for transcript #1: ENST00000376228
Querying Taster for transcript #2: ENST00000383329
Querying Taster for transcript #3: ENST00000396254
Querying Taster for transcript #4: ENST00000539307
MT speed 2.29 s - this script 5.268142 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
HLA-Cpolymorphism_automatic6.5802918669533e-13simple_aaeaffectedN104Ksingle base exchangers17408553show file
HLA-Cpolymorphism_automatic6.5802918669533e-13simple_aaeaffectedN104Ksingle base exchangers17408553show file
HLA-Cpolymorphism_automatic6.5802918669533e-13simple_aaeaffectedN141Ksingle base exchangers17408553show file
HLA-Cpolymorphism_automatic6.5802918669533e-13simple_aaeaffectedN104Ksingle base exchangers17408553show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999342 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr6:31239407G>TN/A show variant in all transcripts   IGV
HGNC symbol HLA-C
Ensembl transcript ID ENST00000376228
Genbank transcript ID NM_002117
UniProt peptide P30501
alteration type single base exchange
alteration region CDS
DNA changes c.312C>A
cDNA.327C>A
g.501C>A
AA changes N104K Score: 94 explain score(s)
position(s) of altered AA
if AA alteration in CDS
104
frameshift no
known variant Reference ID: rs17408553
databasehomozygous (T/T)heterozygousallele carriers
1000G43810621500
ExAC91161453523651
regulatory features CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H2BK5ac, Histone, Histone 2B Lysine 5 Acetylation
H3K18ac, Histone, Histone 3 Lysine 18 Acetylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K79me2, Histone, Histone 3 Lysine 79 di-methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.3370
-0.060
(flanking)-2.940
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased496wt: 0.25 / mu: 0.94wt: GCCTGCGGAACCTGC
mu: GCCTGCGGAAACTGC
 CTGC|ggaa
distance from splice site 32
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      104RQAQADRVSLRNLRGYYNQSEDGS
mutated  not conserved    104RQAQADRVSLRKLRGYYNQSEDG
Ptroglodytes  all identical  ENSPTRG00000041261  104RQAQADRVSLRNLRGYYNQSEDG
Mmulatta  not conserved  ENSMMUG00000029841  104THTENFQVNLTLLR-HYNPSEAE
Fcatus  no homologue    
Mmusculus  no homologue    
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
25114REGIONAlpha-1.lost
25308TOPO_DOMExtracellular (Potential).lost
110110CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
115206REGIONAlpha-2.might get lost (downstream of altered splice site)
125125DISULFIDBy similarity.might get lost (downstream of altered splice site)
188188DISULFIDBy similarity.might get lost (downstream of altered splice site)
207298REGIONAlpha-3.might get lost (downstream of altered splice site)
209297DOMAINIg-like C1-type.might get lost (downstream of altered splice site)
227227DISULFIDBy similarity.might get lost (downstream of altered splice site)
283283DISULFIDBy similarity.might get lost (downstream of altered splice site)
299308REGIONConnecting peptide.might get lost (downstream of altered splice site)
309333TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
334366TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1101 / 1101
position (AA) of stopcodon in wt / mu AA sequence 367 / 367
position of stopcodon in wt / mu cDNA 1116 / 1116
poly(A) signal N/A
conservation
nucleotide level for all changes - no scoring up to now
N/A
position of start ATG in wt / mu cDNA 16 / 16
chromosome 6
strand -1
last intron/exon boundary 1112
theoretical NMD boundary in CDS 1046
length of CDS 1101
coding sequence (CDS) position 312
cDNA position
(for ins/del: last normal base / first normal base)
327
gDNA position
(for ins/del: last normal base / first normal base)
501
chromosomal position
(for ins/del: last normal base / first normal base)
31239407
original gDNA sequence snippet GACCGAGTGAGCCTGCGGAACCTGCGCGGCTACTACAACCA
altered gDNA sequence snippet GACCGAGTGAGCCTGCGGAAACTGCGCGGCTACTACAACCA
original cDNA sequence snippet GACCGAGTGAGCCTGCGGAACCTGCGCGGCTACTACAACCA
altered cDNA sequence snippet GACCGAGTGAGCCTGCGGAAACTGCGCGGCTACTACAACCA
wildtype AA sequence MRVMAPRALL LLLSGGLALT ETWACSHSMR YFDTAVSRPG RGEPRFISVG YVDDTQFVRF
DSDAASPRGE PRAPWVEQEG PEYWDRETQK YKRQAQADRV SLRNLRGYYN QSEDGSHTLQ
RMSGCDLGPD GRLLRGYDQS AYDGKDYIAL NEDLRSWTAA DTAAQITQRK LEAARAAEQL
RAYLEGTCVE WLRRYLENGK ETLQRAEPPK THVTHHPLSD HEATLRCWAL GFYPAEITLT
WQRDGEDQTQ DTELVETRPA GDGTFQKWAA VVVPSGQEQR YTCHMQHEGL QEPLTLSWEP
SSQPTIPIMG IVAGLAVLVV LAVLGAVVTA MMCRRKSSGG KGGSCSQAAC SNSAQGSDES
LITCKA*
mutated AA sequence MRVMAPRALL LLLSGGLALT ETWACSHSMR YFDTAVSRPG RGEPRFISVG YVDDTQFVRF
DSDAASPRGE PRAPWVEQEG PEYWDRETQK YKRQAQADRV SLRKLRGYYN QSEDGSHTLQ
RMSGCDLGPD GRLLRGYDQS AYDGKDYIAL NEDLRSWTAA DTAAQITQRK LEAARAAEQL
RAYLEGTCVE WLRRYLENGK ETLQRAEPPK THVTHHPLSD HEATLRCWAL GFYPAEITLT
WQRDGEDQTQ DTELVETRPA GDGTFQKWAA VVVPSGQEQR YTCHMQHEGL QEPLTLSWEP
SSQPTIPIMG IVAGLAVLVV LAVLGAVVTA MMCRRKSSGG KGGSCSQAAC SNSAQGSDES
LITCKA*
speed 0.59 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table
Yum, tasty mutations...

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999342 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr6:31239407G>TN/A show variant in all transcripts   IGV
HGNC symbol HLA-C
Ensembl transcript ID ENST00000396254
Genbank transcript ID N/A
UniProt peptide P30501
alteration type single base exchange
alteration region CDS
DNA changes c.312C>A
cDNA.327C>A
g.501C>A
AA changes N104K Score: 94 explain score(s)
position(s) of altered AA
if AA alteration in CDS
104
frameshift no
known variant Reference ID: rs17408553
databasehomozygous (T/T)heterozygousallele carriers
1000G43810621500
ExAC91161453523651
regulatory features CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H2BK5ac, Histone, Histone 2B Lysine 5 Acetylation
H3K18ac, Histone, Histone 3 Lysine 18 Acetylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K79me2, Histone, Histone 3 Lysine 79 di-methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.3370
-0.060
(flanking)-2.940
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased496wt: 0.25 / mu: 0.94wt: GCCTGCGGAACCTGC
mu: GCCTGCGGAAACTGC
 CTGC|ggaa
distance from splice site 32
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      104RQAQADRVSLRNLRGYYNQSEDGS
mutated  not conserved    104RQAQADRVSLRKLRGYYNQSEDG
Ptroglodytes  all identical  ENSPTRG00000041261  104RQAQADRVSLRNLRGYYNQSEDG
Mmulatta  not conserved  ENSMMUG00000029841  104THTENFQVNLTLLR-HYNPSEAE
Fcatus  no homologue    
Mmusculus  no homologue    
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
25114REGIONAlpha-1.lost
25308TOPO_DOMExtracellular (Potential).lost
110110CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
115206REGIONAlpha-2.might get lost (downstream of altered splice site)
125125DISULFIDBy similarity.might get lost (downstream of altered splice site)
188188DISULFIDBy similarity.might get lost (downstream of altered splice site)
207298REGIONAlpha-3.might get lost (downstream of altered splice site)
209297DOMAINIg-like C1-type.might get lost (downstream of altered splice site)
227227DISULFIDBy similarity.might get lost (downstream of altered splice site)
283283DISULFIDBy similarity.might get lost (downstream of altered splice site)
299308REGIONConnecting peptide.might get lost (downstream of altered splice site)
309333TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
334366TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1194 / 1194
position (AA) of stopcodon in wt / mu AA sequence 398 / 398
position of stopcodon in wt / mu cDNA 1209 / 1209
poly(A) signal N/A
conservation
nucleotide level for all changes - no scoring up to now
N/A
position of start ATG in wt / mu cDNA 16 / 16
chromosome 6
strand -1
last intron/exon boundary 1108
theoretical NMD boundary in CDS 1042
length of CDS 1194
coding sequence (CDS) position 312
cDNA position
(for ins/del: last normal base / first normal base)
327
gDNA position
(for ins/del: last normal base / first normal base)
501
chromosomal position
(for ins/del: last normal base / first normal base)
31239407
original gDNA sequence snippet GACCGAGTGAGCCTGCGGAACCTGCGCGGCTACTACAACCA
altered gDNA sequence snippet GACCGAGTGAGCCTGCGGAAACTGCGCGGCTACTACAACCA
original cDNA sequence snippet GACCGAGTGAGCCTGCGGAACCTGCGCGGCTACTACAACCA
altered cDNA sequence snippet GACCGAGTGAGCCTGCGGAAACTGCGCGGCTACTACAACCA
wildtype AA sequence MRVMAPRALL LLLSGGLALT ETWACSHSMR YFDTAVSRPG RGEPRFISVG YVDDTQFVRF
DSDAASPRGE PRAPWVEQEG PEYWDRETQK YKRQAQADRV SLRNLRGYYN QSEDGSHTLQ
RMSGCDLGPD GRLLRGYDQS AYDGKDYIAL NEDLRSWTAA DTAAQITQRK LEAARAAEQL
RAYLEGTCVE WLRRYLENGK ETLQRAEPPK THVTHHPLSD HEATLRCWAL GFYPAEITLT
WQRDGEDQTQ DTELVETRPA GDGTFQKWAA VVVPSGQEQR YTCHMQHEGL QEPLTLSWEP
SSQPTIPIMG IVAGLAVLVV LAVLGAVVTA MMCRRKSSGR EGVKSGVWAA TVPRALMSLS
SLVKPETAAC VGLRCRISSH LSFVTSRASG ISFCKGT*
mutated AA sequence MRVMAPRALL LLLSGGLALT ETWACSHSMR YFDTAVSRPG RGEPRFISVG YVDDTQFVRF
DSDAASPRGE PRAPWVEQEG PEYWDRETQK YKRQAQADRV SLRKLRGYYN QSEDGSHTLQ
RMSGCDLGPD GRLLRGYDQS AYDGKDYIAL NEDLRSWTAA DTAAQITQRK LEAARAAEQL
RAYLEGTCVE WLRRYLENGK ETLQRAEPPK THVTHHPLSD HEATLRCWAL GFYPAEITLT
WQRDGEDQTQ DTELVETRPA GDGTFQKWAA VVVPSGQEQR YTCHMQHEGL QEPLTLSWEP
SSQPTIPIMG IVAGLAVLVV LAVLGAVVTA MMCRRKSSGR EGVKSGVWAA TVPRALMSLS
SLVKPETAAC VGLRCRISSH LSFVTSRASG ISFCKGT*
speed 0.48 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table
Yum, tasty mutations...

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999342 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr6:31239407G>TN/A show variant in all transcripts   IGV
HGNC symbol HLA-C
Ensembl transcript ID ENST00000539307
Genbank transcript ID N/A
UniProt peptide P30501
alteration type single base exchange
alteration region CDS
DNA changes c.423C>A
cDNA.423C>A
g.501C>A
AA changes N141K Score: 94 explain score(s)
position(s) of altered AA
if AA alteration in CDS
141
frameshift no
known variant Reference ID: rs17408553
databasehomozygous (T/T)heterozygousallele carriers
1000G43810621500
ExAC91161453523651
regulatory features CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H2BK5ac, Histone, Histone 2B Lysine 5 Acetylation
H3K18ac, Histone, Histone 3 Lysine 18 Acetylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K79me2, Histone, Histone 3 Lysine 79 di-methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.3370
-0.060
(flanking)-2.940
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased496wt: 0.25 / mu: 0.94wt: GCCTGCGGAACCTGC
mu: GCCTGCGGAAACTGC
 CTGC|ggaa
distance from splice site 32
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      141RQAQADRVSLRNLRGYYNQSEDGS
mutated  not conserved    141RQAQADRVSLRKLRGYYNQSEDG
Ptroglodytes  all identical  ENSPTRG00000041261  104RQAQADRVSLRNLRGYYNQSEDG
Mmulatta  not conserved  ENSMMUG00000029841  100THTENFQVNLTLLR-HYNPSEAE
Fcatus  no homologue    
Mmusculus  no homologue    
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
25308TOPO_DOMExtracellular (Potential).lost
115206REGIONAlpha-2.lost
188188DISULFIDBy similarity.might get lost (downstream of altered splice site)
207298REGIONAlpha-3.might get lost (downstream of altered splice site)
209297DOMAINIg-like C1-type.might get lost (downstream of altered splice site)
227227DISULFIDBy similarity.might get lost (downstream of altered splice site)
283283DISULFIDBy similarity.might get lost (downstream of altered splice site)
299308REGIONConnecting peptide.might get lost (downstream of altered splice site)
309333TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
334366TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1212 / 1212
position (AA) of stopcodon in wt / mu AA sequence 404 / 404
position of stopcodon in wt / mu cDNA 1212 / 1212
poly(A) signal N/A
conservation
nucleotide level for all changes - no scoring up to now
N/A
position of start ATG in wt / mu cDNA 1 / 1
chromosome 6
strand -1
last intron/exon boundary 1208
theoretical NMD boundary in CDS 1157
length of CDS 1212
coding sequence (CDS) position 423
cDNA position
(for ins/del: last normal base / first normal base)
423
gDNA position
(for ins/del: last normal base / first normal base)
501
chromosomal position
(for ins/del: last normal base / first normal base)
31239407
original gDNA sequence snippet GACCGAGTGAGCCTGCGGAACCTGCGCGGCTACTACAACCA
altered gDNA sequence snippet GACCGAGTGAGCCTGCGGAAACTGCGCGGCTACTACAACCA
original cDNA sequence snippet GACCGAGTGAGCCTGCGGAACCTGCGCGGCTACTACAACCA
altered cDNA sequence snippet GACCGAGTGAGCCTGCGGAAACTGCGCGGCTACTACAACCA
wildtype AA sequence MRVMAPRALL LLLSGGLALT ETWACECGVG REAASAERSE GPPGEPRREV GRAGLSPSSP
PGSHSMRYFD TAVSRPGRGE PRFISVGYVD DTQFVRFDSD AASPRGEPRA PWVEQEGPEY
WDRETQKYKR QAQADRVSLR NLRGYYNQSE DGSHTLQRMS GCDLGPDGRL LRGYDQSAYD
GKDYIALNED LRSWTAADTA AQITQRKLEA ARAAEQLRAY LEGTCVEWLR RYLENGKETL
QRAEPPKTHV THHPLSDHEA TLRCWALGFY PAEITLTWQR DGEDQTQDTE LVETRPAGDG
TFQKWAAVVV PSGQEQRYTC HMQHEGLQEP LTLSWEPSSQ PTIPIMGIVA GLAVLVVLAV
LGAVVTAMMC RRKSSGGKGG SCSQAACSNS AQGSDESLIT CKA*
mutated AA sequence MRVMAPRALL LLLSGGLALT ETWACECGVG REAASAERSE GPPGEPRREV GRAGLSPSSP
PGSHSMRYFD TAVSRPGRGE PRFISVGYVD DTQFVRFDSD AASPRGEPRA PWVEQEGPEY
WDRETQKYKR QAQADRVSLR KLRGYYNQSE DGSHTLQRMS GCDLGPDGRL LRGYDQSAYD
GKDYIALNED LRSWTAADTA AQITQRKLEA ARAAEQLRAY LEGTCVEWLR RYLENGKETL
QRAEPPKTHV THHPLSDHEA TLRCWALGFY PAEITLTWQR DGEDQTQDTE LVETRPAGDG
TFQKWAAVVV PSGQEQRYTC HMQHEGLQEP LTLSWEPSSQ PTIPIMGIVA GLAVLVVLAV
LGAVVTAMMC RRKSSGGKGG SCSQAACSNS AQGSDESLIT CKA*
speed 0.58 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table
Yum, tasty mutations...

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999342 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr6:31239407G>TN/A show variant in all transcripts   IGV
HGNC symbol HLA-C
Ensembl transcript ID ENST00000383329
Genbank transcript ID N/A
UniProt peptide P30501
alteration type single base exchange
alteration region CDS
DNA changes c.312C>A
cDNA.327C>A
g.501C>A
AA changes N104K Score: 94 explain score(s)
position(s) of altered AA
if AA alteration in CDS
104
frameshift no
known variant Reference ID: rs17408553
databasehomozygous (T/T)heterozygousallele carriers
1000G43810621500
ExAC91161453523651
regulatory features CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H2BK5ac, Histone, Histone 2B Lysine 5 Acetylation
H3K18ac, Histone, Histone 3 Lysine 18 Acetylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K79me2, Histone, Histone 3 Lysine 79 di-methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.3370
-0.060
(flanking)-2.940
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased496wt: 0.25 / mu: 0.94wt: GCCTGCGGAACCTGC
mu: GCCTGCGGAAACTGC
 CTGC|ggaa
distance from splice site 32
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      104RQAQADRVSLRNLRGYYNQSEDGS
mutated  not conserved    104RQAQADRVSLRKLRGYYNQSEDG
Ptroglodytes  all identical  ENSPTRG00000041261  104RQAQADRVSLRNLRGYYNQSEDG
Mmulatta  not conserved  ENSMMUG00000029841  104THTENFQVNLTLLR-HYNPSEAE
Fcatus  no homologue    
Mmusculus  no homologue    
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
25114REGIONAlpha-1.lost
25308TOPO_DOMExtracellular (Potential).lost
110110CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
115206REGIONAlpha-2.might get lost (downstream of altered splice site)
125125DISULFIDBy similarity.might get lost (downstream of altered splice site)
188188DISULFIDBy similarity.might get lost (downstream of altered splice site)
207298REGIONAlpha-3.might get lost (downstream of altered splice site)
209297DOMAINIg-like C1-type.might get lost (downstream of altered splice site)
227227DISULFIDBy similarity.might get lost (downstream of altered splice site)
283283DISULFIDBy similarity.might get lost (downstream of altered splice site)
299308REGIONConnecting peptide.might get lost (downstream of altered splice site)
309333TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
334366TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1119 / 1119
position (AA) of stopcodon in wt / mu AA sequence 373 / 373
position of stopcodon in wt / mu cDNA 1134 / 1134
poly(A) signal N/A
conservation
nucleotide level for all changes - no scoring up to now
N/A
position of start ATG in wt / mu cDNA 16 / 16
chromosome 6
strand -1
last intron/exon boundary 1130
theoretical NMD boundary in CDS 1064
length of CDS 1119
coding sequence (CDS) position 312
cDNA position
(for ins/del: last normal base / first normal base)
327
gDNA position
(for ins/del: last normal base / first normal base)
501
chromosomal position
(for ins/del: last normal base / first normal base)
31239407
original gDNA sequence snippet GACCGAGTGAGCCTGCGGAACCTGCGCGGCTACTACAACCA
altered gDNA sequence snippet GACCGAGTGAGCCTGCGGAAACTGCGCGGCTACTACAACCA
original cDNA sequence snippet GACCGAGTGAGCCTGCGGAACCTGCGCGGCTACTACAACCA
altered cDNA sequence snippet GACCGAGTGAGCCTGCGGAAACTGCGCGGCTACTACAACCA
wildtype AA sequence MRVMAPRALL LLLSGGLALT ETWACSHSMR YFDTAVSRPG RGEPRFISVG YVDDTQFVRF
DSDAASPRGE PRAPWVEQEG PEYWDRETQK YKRQAQADRV SLRNLRGYYN QSEDGSHTLQ
RMSGCDLGPD GRLLRGYDQS AYDGKDYIAL NEDLRSWTAA DTAAQITQRK LEAARAAEQL
RAYLEGTCVE WLRRYLENGK ETLQRAEPPK THVTHHPLSD HEATLRCWAL GFYPAEITLT
WQRDGEDQTQ DTELVETRPA GDGTFQKWAA VVVPSGQEQR YTCHMQHEGL QEPLTLSWEP
SSQPTIPIMG IVAGLAVLVV LAVLGAVVTA MMCRRKSSGH FLPTGGKGGS CSQAACSNSA
QGSDESLITC KA*
mutated AA sequence MRVMAPRALL LLLSGGLALT ETWACSHSMR YFDTAVSRPG RGEPRFISVG YVDDTQFVRF
DSDAASPRGE PRAPWVEQEG PEYWDRETQK YKRQAQADRV SLRKLRGYYN QSEDGSHTLQ
RMSGCDLGPD GRLLRGYDQS AYDGKDYIAL NEDLRSWTAA DTAAQITQRK LEAARAAEQL
RAYLEGTCVE WLRRYLENGK ETLQRAEPPK THVTHHPLSD HEATLRCWAL GFYPAEITLT
WQRDGEDQTQ DTELVETRPA GDGTFQKWAA VVVPSGQEQR YTCHMQHEGL QEPLTLSWEP
SSQPTIPIMG IVAGLAVLVV LAVLGAVVTA MMCRRKSSGH FLPTGGKGGS CSQAACSNSA
QGSDESLITC KA*
speed 0.64 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
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Problems