Prediction |
polymorphism |
Model: without_aae, prob: 4.63605388744436e-46 (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) | chr11:5842356A>GN/A
show variant in all transcripts IGV
|
| HGNC symbol | TRIM5 |
| Ensembl transcript ID | ENST00000380027 |
| Genbank transcript ID | N/A |
| UniProt peptide | Q9C035 |
| alteration type | single base exchange |
| alteration region | intron |
| DNA changes | g.117494T>C |
| AA changes | N/A |
position(s) of altered AA
if AA alteration in CDS | N/A |
| frameshift | N/A |
| known variant | Reference ID: rs8181512
| database | homozygous (G/G) | heterozygous | allele carriers |
| 1000G | 546 | 1183 | 1729 |
| ExAC | 16212 | 343 | 16555 |
|
| regulatory features | N/A |
| phyloP / phastCons | | PhyloP | PhastCons |
| (flanking) | 3.972 | 0.986 | | 4.669 | 0.986 | | (flanking) | -0.764 | 0.321 |
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser |
| splice sites | splice site change before start ATG (at aa -146) | | effect | gDNA position | score | detection sequence | exon-intron border | | Acc marginally increased | 117488 | wt: 0.8607 / mu: 0.8796 (marginal change - not scored) | wt: TTGGGATATTGTGTCCTACAAAACGATGAGTGAAAAAAGTG
mu: TTGGGATATTGTGTCCTACAAAACGACGAGTGAAAAAAGTG | acaa|AACG | | Donor increased | 117489 | wt: 0.63 / mu: 0.87 | wt: TACAAAACGATGAGT
mu: TACAAAACGACGAGT | CAAA|acga | | Donor marginally increased | 117496 | wt: 0.9953 / mu: 0.9969 (marginal change - not scored) | wt: CGATGAGTGAAAAAA
mu: CGACGAGTGAAAAAA | ATGA|gtga | | Donor increased | 117486 | wt: 0.31 / mu: 0.52 | wt: TCCTACAAAACGATG
mu: TCCTACAAAACGACG | CTAC|aaaa | | Acc gained | 117486 | 0.32 | mu: GTTTGGGATATTGTGTCCTACAAAACGACGAGTGAAAAAAG | ctac|AAAA | | Donor gained | 117485 | 0.32 | mu: GTCCTACAAAACGAC | CCTA|caaa |
|
| distance from splice site | 34626 |
| Kozak consensus sequence altered? | N/A |
conservation
protein level for non-synonymous changes | N/A |
| protein features | | start (aa) | end (aa) | feature | details | | | 15 | 15 | MUTAGEN | C->A: Abolishes E3 ligase activity. | might get lost (downstream of altered splice site) | | 15 | 59 | ZN_FING | RING-type. | might get lost (downstream of altered splice site) | | 16 | 18 | TURN | | might get lost (downstream of altered splice site) | | 29 | 31 | STRAND | | might get lost (downstream of altered splice site) | | 38 | 45 | HELIX | | might get lost (downstream of altered splice site) | | 46 | 50 | TURN | | might get lost (downstream of altered splice site) | | 56 | 58 | TURN | | might get lost (downstream of altered splice site) | | 64 | 66 | STRAND | | might get lost (downstream of altered splice site) | | 76 | 76 | CONFLICT | I -> L (in Ref. 2; BAB55218). | might get lost (downstream of altered splice site) | | 86 | 86 | MOD_RES | Phosphoserine. | might get lost (downstream of altered splice site) | | 90 | 132 | ZN_FING | B box-type. | might get lost (downstream of altered splice site) | | 92 | 94 | STRAND | | might get lost (downstream of altered splice site) | | 96 | 98 | TURN | | might get lost (downstream of altered splice site) | | 104 | 106 | STRAND | | might get lost (downstream of altered splice site) | | 107 | 109 | TURN | | might get lost (downstream of altered splice site) | | 111 | 113 | STRAND | | might get lost (downstream of altered splice site) | | 115 | 118 | HELIX | | might get lost (downstream of altered splice site) | | 121 | 125 | TURN | | might get lost (downstream of altered splice site) | | 130 | 130 | CONFLICT | L -> P (in Ref. 2; BAB55218). | might get lost (downstream of altered splice site) | | 130 | 241 | COILED | Potential. | might get lost (downstream of altered splice site) | | 281 | 493 | DOMAIN | B30.2/SPRY. | might get lost (downstream of altered splice site) | | 332 | 332 | MUTAGEN | R->K: No effect on HIV-1 and SIVmac infection. | might get lost (downstream of altered splice site) | | 332 | 332 | MUTAGEN | R->D,E,L: Increases strongly cell restriction against HIV-1 infection. | might get lost (downstream of altered splice site) | | 332 | 332 | MUTAGEN | R->A,G,H,P,Q,S: Increases strongly cell restriction against HIV-1 and SIVmac infection. | 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 | 785 / 785 |
| chromosome | 11 |
| strand | -1 |
| last intron/exon boundary | 1680 |
| theoretical NMD boundary in CDS | 845 |
| length of CDS | 981 |
| coding sequence (CDS) position | N/A |
cDNA position
(for ins/del: last normal base / first normal base) | N/A |
gDNA position
(for ins/del: last normal base / first normal base) | 117494 |
chromosomal position
(for ins/del: last normal base / first normal base) | 5842356 |
| original gDNA sequence snippet | TATTGTGTCCTACAAAACGATGAGTGAAAAAAGTGAAAAAA |
| altered gDNA sequence snippet | TATTGTGTCCTACAAAACGACGAGTGAAAAAAGTGAAAAAA |
| original cDNA sequence snippet | N/A |
| altered cDNA sequence snippet | N/A |
| wildtype AA sequence | MASGILVNVK EEVTCPICLE LLTQPLSLDC GHSFCQACLT ANHKKSMLDK GESSCPVCRI
SYQPENIRPN RHVANIVEKL REVKLSPEGQ KVDHCARHGE KLLLFCQEDG KVICWLCERS
QEHRGHHTFL TEEVAREYQV KLQAALEMLR QKQQEAEELE ADIREEKASW KTQIQYDKTN
VLADFEQLRD ILDWEESNEL QNLEKEEEDI LKSLTNSETE MVQQTQSLRE LISDLEHRLQ
GSVMELLQGV DGVIKRTENV TLKKPETFPK NQRRVFRAPD LKGMLEVFRE LTDVRRYWGW
SAMARSRFTA TSTSQIQAIL LPQPPK* |
| mutated AA sequence | N/A |
| speed | 1.02 s |
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