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 3 transcript(s)...
Querying Taster for transcript #1: ENST00000376234
Querying Taster for transcript #2: ENST00000342624
Querying Taster for transcript #3: ENST00000328767
MT speed 0 s - this script 2.829238 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
TMTC4polymorphism_automatic5.64404079028691e-12simple_aaeaffectedV438Isingle base exchangers946837show file
TMTC4polymorphism_automatic5.64404079028691e-12simple_aaeaffectedV308Isingle base exchangers946837show file
TMTC4polymorphism_automatic1.26429977598264e-11simple_aaeaffectedV419Isingle base exchangers946837show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999994356 (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) chr13:101287340C>TN/A show variant in all transcripts   IGV
HGNC symbol TMTC4
Ensembl transcript ID ENST00000342624
Genbank transcript ID NM_032813
UniProt peptide Q5T4D3
alteration type single base exchange
alteration region CDS
DNA changes c.1312G>A
cDNA.1571G>A
g.40008G>A
AA changes V438I Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 438
frameshift no
known variant Reference ID: rs946837
databasehomozygous (T/T)heterozygousallele carriers
1000G43310841517
ExAC76751741725092
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.0280.008
0.7640.007
(flanking)-0.9470.004
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased40011wt: 0.21 / mu: 0.36wt: TCCTCTACCTCCCCAGCGTTGGGTACTGTGTGCTGCTGACT
mu: TCCTCTACCTCCCCAGCATTGGGTACTGTGTGCTGCTGACT		 gttg|GGTA
Acc marginally increased40006wt: 0.4101 / mu: 0.4186 (marginal change - not scored)wt: GCGTGTCCTCTACCTCCCCAGCGTTGGGTACTGTGTGCTGC
mu: GCGTGTCCTCTACCTCCCCAGCATTGGGTACTGTGTGCTGC		 ccag|CGTT
Acc marginally increased40009wt: 0.3237 / mu: 0.3243 (marginal change - not scored)wt: TGTCCTCTACCTCCCCAGCGTTGGGTACTGTGTGCTGCTGA
mu: TGTCCTCTACCTCCCCAGCATTGGGTACTGTGTGCTGCTGA		 gcgt|TGGG
Donor marginally increased40005wt: 0.8341 / mu: 0.8538 (marginal change - not scored)wt: TCCCCAGCGTTGGGT
mu: TCCCCAGCATTGGGT		 CCCA|gcgt
distance from splice site 63
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      438VVAERVLYLPSVGYCVLLTFGFGA
mutated  all conserved    438VVAERVLYLPSIGYCVLLTFGFG
Ptroglodytes  all identical  ENSPTRG00000006004  402VVAERVLYLPSVGYCVLLTFGFG
Mmulatta  no homologue    
Fcatus  not conserved  ENSFCAG00000007231  437VVAERVLYLPSAGYCMLLT-GFG
Mmusculus  not conserved  ENSMUSG00000041594  419VVAERVLYLPSAGYCVLLTFGFG
Ggallus  no homologue    
Trubripes  not conserved  ENSTRUG00000011988  419VIAERVLYLSSAGYCLLLAFAFG
Drerio  not conserved  ENSDARG00000020447  416VIAERVLYLSSAGYCLILAYA
Dmelanogaster  all conserved  FBgn0038324  378VIAERTLYVPSIGFCLLSIYGFLYWYD
Celegans  not conserved  F38B6.6  372SIAERVLYLPSAGFCLLCAIIFK
Xtropicalis  all identical  ENSXETG00000020677  417VVAERVLYLPSVGYCVLFTYGYS
protein features
start (aa)end (aa)featuredetails 
441441CONFLICTL -> P (in Ref. 1; BAB55179).might get lost (downstream of altered splice site)
441461TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
448481REPEATTPR 1.might get lost (downstream of altered splice site)
482515REPEATTPR 2.might get lost (downstream of altered splice site)
504504CONFLICTY -> N (in Ref. 1; BAB55179).might get lost (downstream of altered splice site)
517549REPEATTPR 3.might get lost (downstream of altered splice site)
550583REPEATTPR 4.might get lost (downstream of altered splice site)
584617REPEATTPR 5.might get lost (downstream of altered splice site)
619651REPEATTPR 6.might get lost (downstream of altered splice site)
652685REPEATTPR 7.might get lost (downstream of altered splice site)
667667CONFLICTK -> E (in Ref. 1; BAB55179).might get lost (downstream of altered splice site)
686719REPEATTPR 8.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2283 / 2283
position (AA) of stopcodon in wt / mu AA sequence 761 / 761
position of stopcodon in wt / mu cDNA 2542 / 2542
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 260 / 260
chromosome 13
strand -1
last intron/exon boundary 2394
theoretical NMD boundary in CDS 2084
length of CDS 2283
coding sequence (CDS) position 1312
cDNA position
(for ins/del: last normal base / first normal base)		 1571
gDNA position
(for ins/del: last normal base / first normal base)		 40008
chromosomal position
(for ins/del: last normal base / first normal base)		 101287340
original gDNA sequence snippet GTGTCCTCTACCTCCCCAGCGTTGGGTACTGTGTGCTGCTG
altered gDNA sequence snippet GTGTCCTCTACCTCCCCAGCATTGGGTACTGTGTGCTGCTG
original cDNA sequence snippet GTGTCCTCTACCTCCCCAGCGTTGGGTACTGTGTGCTGCTG
altered cDNA sequence snippet GTGTCCTCTACCTCCCCAGCATTGGGTACTGTGTGCTGCTG
wildtype AA sequence MIPNQHNAGA GSHQPAVFRM AVLDTDLDHI LPSSVLPPFW AKLVVGSVAI VCFARSYDGD
FVFDDSEAIV NNKDLQAETP LGDLWHHDFW GSRLSSNTSH KSYRPLTVLT FRINYYLSGG
FHPVGFHVVN ILLHSGISVL MVDVFSVLFG GLQYTSKGRR LHLAPRASLL AALLFAVHPV
HTECVAGVVG RADLLCALFF LLSFLGYCKA FRESNKEGAH SSTFWVLLSI FLGAVAMLCK
EQGITVLGLN AVFDILVIGK FNVLEIVQKV LHKDKSLENL GMLRNGGLLF RMTLLTSGGA
GMLYVRWRIM GTGPPAFTEV DNPASFADSM LVRAVNYNYY YSLNAWLLLC PWWLCFDWSM
GCIPLIKSIS DWRVIALAAL WFCLIGLICQ ALCSEDGHKR RILTLGLGFL VIPFLPASNL
FFRVGFVVAE RVLYLPSVGY CVLLTFGFGA LSKHTKKKKL IAAVVLGILF INTLRCVLRS
GEWRSEEQLF RSALSVCPLN AKVHYNIGKN LADKGNQTAA IRYYREAVRL NPKYVHAMNN
LGNILKERNE LQEAEELLSL AVQIQPDFAA AWMNLGIVQN SLKRFEAAEQ SYRTAIKHRR
KYPDCYYNLG RLYADLNRHV DALNAWRNAT VLKPEHSLAW NNMIILLDNT GNLAQAEAVG
REALELIPND HSLMFSLANV LGKSQKYKES EALFLKAIKA NPNAASYHGN LAVLYHRWGH
LDLAKKHYEI SLQLDPTASG TKENYGLLRR KLELMQKKAV *
mutated AA sequence MIPNQHNAGA GSHQPAVFRM AVLDTDLDHI LPSSVLPPFW AKLVVGSVAI VCFARSYDGD
FVFDDSEAIV NNKDLQAETP LGDLWHHDFW GSRLSSNTSH KSYRPLTVLT FRINYYLSGG
FHPVGFHVVN ILLHSGISVL MVDVFSVLFG GLQYTSKGRR LHLAPRASLL AALLFAVHPV
HTECVAGVVG RADLLCALFF LLSFLGYCKA FRESNKEGAH SSTFWVLLSI FLGAVAMLCK
EQGITVLGLN AVFDILVIGK FNVLEIVQKV LHKDKSLENL GMLRNGGLLF RMTLLTSGGA
GMLYVRWRIM GTGPPAFTEV DNPASFADSM LVRAVNYNYY YSLNAWLLLC PWWLCFDWSM
GCIPLIKSIS DWRVIALAAL WFCLIGLICQ ALCSEDGHKR RILTLGLGFL VIPFLPASNL
FFRVGFVVAE RVLYLPSIGY CVLLTFGFGA LSKHTKKKKL IAAVVLGILF INTLRCVLRS
GEWRSEEQLF RSALSVCPLN AKVHYNIGKN LADKGNQTAA IRYYREAVRL NPKYVHAMNN
LGNILKERNE LQEAEELLSL AVQIQPDFAA AWMNLGIVQN SLKRFEAAEQ SYRTAIKHRR
KYPDCYYNLG RLYADLNRHV DALNAWRNAT VLKPEHSLAW NNMIILLDNT GNLAQAEAVG
REALELIPND HSLMFSLANV LGKSQKYKES EALFLKAIKA NPNAASYHGN LAVLYHRWGH
LDLAKKHYEI SLQLDPTASG TKENYGLLRR KLELMQKKAV *
speed 0.39 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: 0.999999999994356 (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) chr13:101287340C>TN/A show variant in all transcripts   IGV
HGNC symbol TMTC4
Ensembl transcript ID ENST00000328767
Genbank transcript ID N/A
UniProt peptide Q5T4D3
alteration type single base exchange
alteration region CDS
DNA changes c.922G>A
cDNA.1007G>A
g.40008G>A
AA changes V308I Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 308
frameshift no
known variant Reference ID: rs946837
databasehomozygous (T/T)heterozygousallele carriers
1000G43310841517
ExAC76751741725092
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.0280.008
0.7640.007
(flanking)-0.9470.004
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased40011wt: 0.21 / mu: 0.36wt: TCCTCTACCTCCCCAGCGTTGGGTACTGTGTGCTGCTGACT
mu: TCCTCTACCTCCCCAGCATTGGGTACTGTGTGCTGCTGACT		 gttg|GGTA
Acc marginally increased40006wt: 0.4101 / mu: 0.4186 (marginal change - not scored)wt: GCGTGTCCTCTACCTCCCCAGCGTTGGGTACTGTGTGCTGC
mu: GCGTGTCCTCTACCTCCCCAGCATTGGGTACTGTGTGCTGC		 ccag|CGTT
Acc marginally increased40009wt: 0.3237 / mu: 0.3243 (marginal change - not scored)wt: TGTCCTCTACCTCCCCAGCGTTGGGTACTGTGTGCTGCTGA
mu: TGTCCTCTACCTCCCCAGCATTGGGTACTGTGTGCTGCTGA		 gcgt|TGGG
Donor marginally increased40005wt: 0.8341 / mu: 0.8538 (marginal change - not scored)wt: TCCCCAGCGTTGGGT
mu: TCCCCAGCATTGGGT		 CCCA|gcgt
distance from splice site 63
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      308VVAERVLYLPSVGYCVLLTFGFGA
mutated  all conserved    308RVLYLPSIGYCVLLTFGFG
Ptroglodytes  all identical  ENSPTRG00000006004  402VVAERVLYLPSVGYCVLLTFGFG
Mmulatta  no homologue    
Fcatus  not conserved  ENSFCAG00000007231  437VVAERVLYLPSAGYCMLLT-GFG
Mmusculus  not conserved  ENSMUSG00000041594  419VVAERVLYLPSAGYCVLLTFGFG
Ggallus  no homologue    
Trubripes  not conserved  ENSTRUG00000011988  419VIAERVLYLSSAGYCLLLAFAFGH
Drerio  not conserved  ENSDARG00000020447  416VIAERVLYLSSAGYCLILAYAVG
Dmelanogaster  all conserved  FBgn0038324  378VIAERTLYVPSIGFCLLSIYGFLYWYD
Celegans  not conserved  F38B6.6  372SIAERVLYLPSAGFCLLCAIIFK
Xtropicalis  all identical  ENSXETG00000020677  417VVAERVLYLPSVGYCVLFTYGYS
protein features
start (aa)end (aa)featuredetails 
318337TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
355375TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
383403TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
413433TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
441441CONFLICTL -> P (in Ref. 1; BAB55179).might get lost (downstream of altered splice site)
441461TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
448481REPEATTPR 1.might get lost (downstream of altered splice site)
482515REPEATTPR 2.might get lost (downstream of altered splice site)
504504CONFLICTY -> N (in Ref. 1; BAB55179).might get lost (downstream of altered splice site)
517549REPEATTPR 3.might get lost (downstream of altered splice site)
550583REPEATTPR 4.might get lost (downstream of altered splice site)
584617REPEATTPR 5.might get lost (downstream of altered splice site)
619651REPEATTPR 6.might get lost (downstream of altered splice site)
652685REPEATTPR 7.might get lost (downstream of altered splice site)
667667CONFLICTK -> E (in Ref. 1; BAB55179).might get lost (downstream of altered splice site)
686719REPEATTPR 8.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1893 / 1893
position (AA) of stopcodon in wt / mu AA sequence 631 / 631
position of stopcodon in wt / mu cDNA 1978 / 1978
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 86 / 86
chromosome 13
strand -1
last intron/exon boundary 1830
theoretical NMD boundary in CDS 1694
length of CDS 1893
coding sequence (CDS) position 922
cDNA position
(for ins/del: last normal base / first normal base)		 1007
gDNA position
(for ins/del: last normal base / first normal base)		 40008
chromosomal position
(for ins/del: last normal base / first normal base)		 101287340
original gDNA sequence snippet GTGTCCTCTACCTCCCCAGCGTTGGGTACTGTGTGCTGCTG
altered gDNA sequence snippet GTGTCCTCTACCTCCCCAGCATTGGGTACTGTGTGCTGCTG
original cDNA sequence snippet GTGTCCTCTACCTCCCCAGCGTTGGGTACTGTGTGCTGCTG
altered cDNA sequence snippet GTGTCCTCTACCTCCCCAGCATTGGGTACTGTGTGCTGCTG
wildtype AA sequence MAVLDTDLDH ILPSSVLPPF WAKLVVGSVA IVCFARSYDG DFVFDDSEAI VNNKVAGVVG
RADLLCALFF LLSFLGYCKA FRESNKEGAH SSTFWVLLSI FLGAVAMLCK EQGITVLGLN
AVFDILVIGK FNVLEIVQKV LHKDKSLENL GMLRNGGLLF RMTLLTSGGA GMLYVRWRIM
GTGPPAFTEV DNPASFADSM LVRAVNYNYY YSLNAWLLLC PWWLCFDWSM GCIPLIKSIS
DWRVIALAAL WFCLIGLICQ ALCSEDGHKR RILTLGLGFL VIPFLPASNL FFRVGFVVAE
RVLYLPSVGY CVLLTFGFGA LSKHTKKKKL IAAVVLGILF INTLRCVLRS GEWRSEEQLF
RSALSVCPLN AKVHYNIGKN LADKGNQTAA IRYYREAVRL NPKYVHAMNN LGNILKERNE
LQEAEELLSL AVQIQPDFAA AWMNLGIVQN SLKRFEAAEQ SYRTAIKHRR KYPDCYYNLG
RLYADLNRHV DALNAWRNAT VLKPEHSLAW NNMIILLDNT GNLAQAEAVG REALELIPND
HSLMFSLANV LGKSQKYKES EALFLKAIKA NPNAASYHGN LAVLYHRWGH LDLAKKHYEI
SLQLDPTASG TKENYGLLRR KLELMQKKAV *
mutated AA sequence MAVLDTDLDH ILPSSVLPPF WAKLVVGSVA IVCFARSYDG DFVFDDSEAI VNNKVAGVVG
RADLLCALFF LLSFLGYCKA FRESNKEGAH SSTFWVLLSI FLGAVAMLCK EQGITVLGLN
AVFDILVIGK FNVLEIVQKV LHKDKSLENL GMLRNGGLLF RMTLLTSGGA GMLYVRWRIM
GTGPPAFTEV DNPASFADSM LVRAVNYNYY YSLNAWLLLC PWWLCFDWSM GCIPLIKSIS
DWRVIALAAL WFCLIGLICQ ALCSEDGHKR RILTLGLGFL VIPFLPASNL FFRVGFVVAE
RVLYLPSIGY CVLLTFGFGA LSKHTKKKKL IAAVVLGILF INTLRCVLRS GEWRSEEQLF
RSALSVCPLN AKVHYNIGKN LADKGNQTAA IRYYREAVRL NPKYVHAMNN LGNILKERNE
LQEAEELLSL AVQIQPDFAA AWMNLGIVQN SLKRFEAAEQ SYRTAIKHRR KYPDCYYNLG
RLYADLNRHV DALNAWRNAT VLKPEHSLAW NNMIILLDNT GNLAQAEAVG REALELIPND
HSLMFSLANV LGKSQKYKES EALFLKAIKA NPNAASYHGN LAVLYHRWGH LDLAKKHYEI
SLQLDPTASG TKENYGLLRR KLELMQKKAV *
speed 0.38 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: 0.999999999987357 (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) chr13:101287340C>TN/A show variant in all transcripts   IGV
HGNC symbol TMTC4
Ensembl transcript ID ENST00000376234
Genbank transcript ID NM_001079669
UniProt peptide Q5T4D3
alteration type single base exchange
alteration region CDS
DNA changes c.1255G>A
cDNA.1445G>A
g.40008G>A
AA changes V419I Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 419
frameshift no
known variant Reference ID: rs946837
databasehomozygous (T/T)heterozygousallele carriers
1000G43310841517
ExAC76751741725092
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.0280.008
0.7640.007
(flanking)-0.9470.004
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased40011wt: 0.21 / mu: 0.36wt: TCCTCTACCTCCCCAGCGTTGGGTACTGTGTGCTGCTGACT
mu: TCCTCTACCTCCCCAGCATTGGGTACTGTGTGCTGCTGACT		 gttg|GGTA
Acc marginally increased40006wt: 0.4101 / mu: 0.4186 (marginal change - not scored)wt: GCGTGTCCTCTACCTCCCCAGCGTTGGGTACTGTGTGCTGC
mu: GCGTGTCCTCTACCTCCCCAGCATTGGGTACTGTGTGCTGC		 ccag|CGTT
Acc marginally increased40009wt: 0.3237 / mu: 0.3243 (marginal change - not scored)wt: TGTCCTCTACCTCCCCAGCGTTGGGTACTGTGTGCTGCTGA
mu: TGTCCTCTACCTCCCCAGCATTGGGTACTGTGTGCTGCTGA		 gcgt|TGGG
Donor marginally increased40005wt: 0.8341 / mu: 0.8538 (marginal change - not scored)wt: TCCCCAGCGTTGGGT
mu: TCCCCAGCATTGGGT		 CCCA|gcgt
distance from splice site 63
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      419VVAERVLYLPSVGYCVLLTFGFGA
mutated  all conserved    419VVAERVLYLPSIGYCVLLTFGFG
Ptroglodytes  all identical  ENSPTRG00000006004  402VVAERVLYLPSVGYCVLLTFGFG
Mmulatta  no homologue    
Fcatus  not conserved  ENSFCAG00000007231  437VVAERVLYLPSAGYCMLLT-GFG
Mmusculus  not conserved  ENSMUSG00000041594  419VVAERVLYLPSAGYCVLLTFGFG
Ggallus  no homologue    
Trubripes  not conserved  ENSTRUG00000011988  419VIAERVLYLSSAGYCLLLAFAFG
Drerio  not conserved  ENSDARG00000020447  416VIAERVLYLSSAGYCLILAYA
Dmelanogaster  all conserved  FBgn0038324  378VIAERTLYVPSIGFCLLSIYGFLYWYD
Celegans  not conserved  F38B6.6  372SIAERVLYLPSAGFCLLCAIIFK
Xtropicalis  all identical  ENSXETG00000020677  417VVAERVLYLPSVGYCVLFTYGYS
protein features
start (aa)end (aa)featuredetails 
413433TRANSMEMHelical; (Potential).lost
441441CONFLICTL -> P (in Ref. 1; BAB55179).might get lost (downstream of altered splice site)
441461TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
448481REPEATTPR 1.might get lost (downstream of altered splice site)
482515REPEATTPR 2.might get lost (downstream of altered splice site)
504504CONFLICTY -> N (in Ref. 1; BAB55179).might get lost (downstream of altered splice site)
517549REPEATTPR 3.might get lost (downstream of altered splice site)
550583REPEATTPR 4.might get lost (downstream of altered splice site)
584617REPEATTPR 5.might get lost (downstream of altered splice site)
619651REPEATTPR 6.might get lost (downstream of altered splice site)
652685REPEATTPR 7.might get lost (downstream of altered splice site)
667667CONFLICTK -> E (in Ref. 1; BAB55179).might get lost (downstream of altered splice site)
686719REPEATTPR 8.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2226 / 2226
position (AA) of stopcodon in wt / mu AA sequence 742 / 742
position of stopcodon in wt / mu cDNA 2416 / 2416
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 191 / 191
chromosome 13
strand -1
last intron/exon boundary 2268
theoretical NMD boundary in CDS 2027
length of CDS 2226
coding sequence (CDS) position 1255
cDNA position
(for ins/del: last normal base / first normal base)		 1445
gDNA position
(for ins/del: last normal base / first normal base)		 40008
chromosomal position
(for ins/del: last normal base / first normal base)		 101287340
original gDNA sequence snippet GTGTCCTCTACCTCCCCAGCGTTGGGTACTGTGTGCTGCTG
altered gDNA sequence snippet GTGTCCTCTACCTCCCCAGCATTGGGTACTGTGTGCTGCTG
original cDNA sequence snippet GTGTCCTCTACCTCCCCAGCGTTGGGTACTGTGTGCTGCTG
altered cDNA sequence snippet GTGTCCTCTACCTCCCCAGCATTGGGTACTGTGTGCTGCTG
wildtype AA sequence MAVLDTDLDH ILPSSVLPPF WAKLVVGSVA IVCFARSYDG DFVFDDSEAI VNNKDLQAET
PLGDLWHHDF WGSRLSSNTS HKSYRPLTVL TFRINYYLSG GFHPVGFHVV NILLHSGISV
LMVDVFSVLF GGLQYTSKGR RLHLAPRASL LAALLFAVHP VHTECVAGVV GRADLLCALF
FLLSFLGYCK AFRESNKEGA HSSTFWVLLS IFLGAVAMLC KEQGITVLGL NAVFDILVIG
KFNVLEIVQK VLHKDKSLEN LGMLRNGGLL FRMTLLTSGG AGMLYVRWRI MGTGPPAFTE
VDNPASFADS MLVRAVNYNY YYSLNAWLLL CPWWLCFDWS MGCIPLIKSI SDWRVIALAA
LWFCLIGLIC QALCSEDGHK RRILTLGLGF LVIPFLPASN LFFRVGFVVA ERVLYLPSVG
YCVLLTFGFG ALSKHTKKKK LIAAVVLGIL FINTLRCVLR SGEWRSEEQL FRSALSVCPL
NAKVHYNIGK NLADKGNQTA AIRYYREAVR LNPKYVHAMN NLGNILKERN ELQEAEELLS
LAVQIQPDFA AAWMNLGIVQ NSLKRFEAAE QSYRTAIKHR RKYPDCYYNL GRLYADLNRH
VDALNAWRNA TVLKPEHSLA WNNMIILLDN TGNLAQAEAV GREALELIPN DHSLMFSLAN
VLGKSQKYKE SEALFLKAIK ANPNAASYHG NLAVLYHRWG HLDLAKKHYE ISLQLDPTAS
GTKENYGLLR RKLELMQKKA V*
mutated AA sequence MAVLDTDLDH ILPSSVLPPF WAKLVVGSVA IVCFARSYDG DFVFDDSEAI VNNKDLQAET
PLGDLWHHDF WGSRLSSNTS HKSYRPLTVL TFRINYYLSG GFHPVGFHVV NILLHSGISV
LMVDVFSVLF GGLQYTSKGR RLHLAPRASL LAALLFAVHP VHTECVAGVV GRADLLCALF
FLLSFLGYCK AFRESNKEGA HSSTFWVLLS IFLGAVAMLC KEQGITVLGL NAVFDILVIG
KFNVLEIVQK VLHKDKSLEN LGMLRNGGLL FRMTLLTSGG AGMLYVRWRI MGTGPPAFTE
VDNPASFADS MLVRAVNYNY YYSLNAWLLL CPWWLCFDWS MGCIPLIKSI SDWRVIALAA
LWFCLIGLIC QALCSEDGHK RRILTLGLGF LVIPFLPASN LFFRVGFVVA ERVLYLPSIG
YCVLLTFGFG ALSKHTKKKK LIAAVVLGIL FINTLRCVLR SGEWRSEEQL FRSALSVCPL
NAKVHYNIGK NLADKGNQTA AIRYYREAVR LNPKYVHAMN NLGNILKERN ELQEAEELLS
LAVQIQPDFA AAWMNLGIVQ NSLKRFEAAE QSYRTAIKHR RKYPDCYYNL GRLYADLNRH
VDALNAWRNA TVLKPEHSLA WNNMIILLDN TGNLAQAEAV GREALELIPN DHSLMFSLAN
VLGKSQKYKE SEALFLKAIK ANPNAASYHG NLAVLYHRWG HLDLAKKHYE ISLQLDPTAS
GTKENYGLLR RKLELMQKKA V*
speed 0.40 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