Prediction |
polymorphism |
Model: without_aae, prob: 2.39255240982173e-06 (classification due to TGP/ExAC,
real probability is shown anyway)
(explain) |
| Summary |
- 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) | chr5:70751818T>GN/A
show variant in all transcripts IGV
|
| HGNC symbol | BDP1 |
| Ensembl transcript ID | ENST00000380675 |
| Genbank transcript ID | N/A |
| UniProt peptide | A6H8Y1 |
| alteration type | single base exchange |
| alteration region | 5'UTR |
| DNA changes | cDNA.377T>G
g.377T>G |
| AA changes | N/A |
position(s) of altered AA
if AA alteration in CDS | N/A |
| frameshift | N/A |
| known variant | Reference ID: rs3748043
| database | homozygous (G/G) | heterozygous | allele carriers |
| 1000G | 1564 | 769 | 2333 |
| ExAC | - | - | - |
|
| regulatory features | CTCF, Transcription Factor, CCCTC-binding factor
Cmyc, Transcription Factor, Cmyc TF binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site
ELF1, Transcription Factor, ELF1 Transcription Factor Binding
H2AZ, Histone, Histone 2A variant Z
H2BK120ac, Histone, Histone 2B Lysine 120 Acetylation
H2BK20ac, Histone, Histone 2B Lysine 20 Acetylation
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
H3K4ac, Histone, Histone 3 Lysine 4 Acetylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
Max, Transcription Factor, Max TF binding
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
Sin3Ak20, Transcription Factor, Sin3Ak20 Transcription Factor Binding
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
Yy1, Transcription Factor, Yy1 Transcription Factor Binding |
| phyloP / phastCons | | PhyloP | PhastCons |
| (flanking) | 0.754 | 0.358 | | -0.332 | 0.346 | | (flanking) | 3.351 | 0.679 |
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser |
| splice sites | splice site change before start ATG (at aa -1827) | | effect | gDNA position | score | detection sequence | exon-intron border | | Donor gained | 371 | 0.70 | mu: AGGCCGCCGGAGCCT | GCCG|ccgg |
|
| distance from splice site | 99 |
| Kozak consensus sequence altered? | no |
conservation
protein level for non-synonymous changes | N/A |
| protein features | | start (aa) | end (aa) | feature | details | | | 1 | 299 | REGION | Interaction with ZBTB43. | might get lost (downstream of altered splice site) | | 8 | 8 | CONFLICT | S -> N (in Ref. 9; AAG09268). | might get lost (downstream of altered splice site) | | 84 | 119 | COMPBIAS | Ser-rich. | might get lost (downstream of altered splice site) | | 144 | 177 | COILED | Potential. | might get lost (downstream of altered splice site) | | 233 | 233 | CONFLICT | E -> G (in Ref. 1; AAG30221/AAG30220). | might get lost (downstream of altered splice site) | | 295 | 345 | DOMAIN | Myb-like. | might get lost (downstream of altered splice site) | | 355 | 470 | REGION | Required for phosphorylation by CSNK2A1. | might get lost (downstream of altered splice site) | | 390 | 390 | MUTAGEN | S->A: Not phosphorylated by CSNK2A1; when associated with A-426; A-431; A-437 and A-446. CK2 treatment constitutively activates for U6 transcription; when associated with A-426; A-431; A-437 and A-446. | might get lost (downstream of altered splice site) | | 426 | 426 | MUTAGEN | S->A: Not phosphorylated by CSNK2A1; when associated with A-390; A-431; A-437 and A-446. CK2 treatment constitutively activates for U6 transcription; when associated with A-390; A-431; A-437 and A-446. | might get lost (downstream of altered splice site) | | 431 | 431 | MUTAGEN | S->A: Not phosphorylated by CSNK2A1; when associated with A-390; A-426; A-437 and A-446. CK2 treatment constitutively activates for U6 transcription; when associated with A-390; A-426; A-437 and A-446. | might get lost (downstream of altered splice site) | | 437 | 437 | MUTAGEN | T->A: Not phosphorylated by CSNK2A1; when associated with A-390; A-426; A-431 and A-446. CK2 treatment constitutively activates for U6 transcription; when associated with A-390; A-426; A-431 and A-446. | might get lost (downstream of altered splice site) | | 446 | 446 | MUTAGEN | S->A: Not phosphorylated by CSNK2A1; when associated with A-390; A-426; A-431 and A-437. CK2 treatment constitutively activates for U6 transcription; when associated with A-390; A-426; A-431 and A-437. | might get lost (downstream of altered splice site) | | 575 | 575 | CONFLICT | R -> K (in Ref. 10; BAB71602). | might get lost (downstream of altered splice site) | | 683 | 683 | CONFLICT | V -> D (in Ref. 2; CAC21448). | might get lost (downstream of altered splice site) | | 823 | 877 | REPEAT | 1; approximate. | might get lost (downstream of altered splice site) | | 823 | 1327 | REGION | 9 X 55 AA repeats of G-R-R-X-I-S-P-X-E-N- G-X-E-E-V-K-P-X-X-E-M-E-T-D-L-K-X-T-G-R- E-X-X-X-R-E-K-T-X-E-X-X-D-A-X-E-E-I-D-X- D-L-E-E-T. | might get lost (downstream of altered splice site) | | 878 | 932 | REPEAT | 2. | might get lost (downstream of altered splice site) | | 881 | 881 | CONFLICT | A -> T (in Ref. 9; AAG09268). | might get lost (downstream of altered splice site) | | 915 | 915 | MOD_RES | Phosphothreonine. | might get lost (downstream of altered splice site) | | 933 | 987 | REPEAT | 3. | might get lost (downstream of altered splice site) | | 973 | 973 | CONFLICT | V -> G (in Ref. 2; CAC21448/CAC04245). | might get lost (downstream of altered splice site) | | 988 | 1040 | REPEAT | 4. | might get lost (downstream of altered splice site) | | 1009 | 1009 | CONFLICT | E -> G (in Ref. 1; AAG30221/AAG30220). | might get lost (downstream of altered splice site) | | 1041 | 1094 | REPEAT | 5. | might get lost (downstream of altered splice site) | | 1078 | 1103 | COILED | Potential. | might get lost (downstream of altered splice site) | | 1095 | 1148 | REPEAT | 6. | might get lost (downstream of altered splice site) | | 1149 | 1203 | REPEAT | 7. | might get lost (downstream of altered splice site) | | 1204 | 1257 | REPEAT | 8; approximate. | might get lost (downstream of altered splice site) | | 1223 | 1284 | COILED | Potential. | might get lost (downstream of altered splice site) | | 1258 | 1327 | REPEAT | 9; approximate. | might get lost (downstream of altered splice site) | | 2196 | 2196 | MOD_RES | Phosphoserine. | might get lost (downstream of altered splice site) | | 2580 | 2580 | CONFLICT | T -> A (in Ref. 6; CAE46010). | might get lost (downstream of altered splice site) |
|
| length of protein | N/A |
| AA sequence altered | N/A |
| position of stopcodon in wt / mu CDS | N/A |
| position (AA) of stopcodon in wt / mu AA sequence | N/A |
| position of stopcodon in wt / mu cDNA | N/A |
| 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 | 5853 / 5853 |
| chromosome | 5 |
| strand | 1 |
| last intron/exon boundary | 7817 |
| theoretical NMD boundary in CDS | 1914 |
| length of CDS | 1392 |
| coding sequence (CDS) position | N/A |
cDNA position
(for ins/del: last normal base / first normal base) | 377 |
gDNA position
(for ins/del: last normal base / first normal base) | 377 |
chromosomal position
(for ins/del: last normal base / first normal base) | 70751818 |
| original gDNA sequence snippet | GAGTCTCCCAGGCCGCCGGATCCTGCCACGGACTCTGCTTC |
| altered gDNA sequence snippet | GAGTCTCCCAGGCCGCCGGAGCCTGCCACGGACTCTGCTTC |
| original cDNA sequence snippet | GAGTCTCCCAGGCCGCCGGATCCTGCCACGGACTCTGCTTC |
| altered cDNA sequence snippet | GAGTCTCCCAGGCCGCCGGAGCCTGCCACGGACTCTGCTTC |
| wildtype AA sequence | MLVTLRASQE EDDDADDFES DYEEESYHLA PEEVNKAPVF VPVGLRSPEP VSAQIEETME
ELEITVNVPD VGCIAVVEHE LPNTDVTTEE MKQEENLSVP FEMTTSEHIQ DEPGTNDGST
EAAITLLTMG DLVLQSEISS EQGDGVCIIP HVHSKDKSHI PSSLDNVNHK IVHECQELSS
PVITTSPASF EENKIVLEEQ SSREEISLME KVKENATPTR NTISKVTSNL RIRSRLAKPK
PNLEKTLGTN RLDDYQEVSS LCVTKGAEME TQRETEKNAS KATELENKNL GPVTTAENKD
QSKLACVHGI KGTSISSEVN LTERNENQEE SSQEVHMLSV APVASSETGP CTLGLDRGLG
ENSVEEPQIK DSKGDSVLTL PVPEYTPTSI PEVQQENIIN PQDLTVFVYQ QLQLVKMPWV
YLFLEEIILK SRLIIWILYL GRDFNAGLIK MTTFLLPKNV HSL* |
| mutated AA sequence | N/A |
| speed | 0.65 s |
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