HsaINT0171750 @ hg19
Intron Retention
Gene
ENSG00000082512 | TRAF5
Description
TNF receptor-associated factor 5 [Source:HGNC Symbol;Acc:12035]
Coordinates
chr1:211544644-211548286:+
Coord C1 exon
chr1:211544644-211544812
Coord A exon
chr1:211544813-211545469
Coord C2 exon
chr1:211545470-211548286
Length
657 bp
Sequences
Splice sites
5' ss Seq
TAGGTATGT
5' ss Score
7.76
3' ss Seq
TTTTTTTTTCTTATTTGCAGCCG
3' ss Score
10.81
Exon sequences
Seq C1 exon
GTTTTTGCCAGTCACATTGACAAGTCAGCTTGGCTAGAAGCTCAAGTGCATCAATTATTACAAATGGTTAACCAGCAACAAAATAAATTTGACCTGAGACCTTTGATGGAAGCAGTTGATACAGTGAAACAGAAAATTACCCTGCTAGAAAACAATGATCAAAGATTAG
Seq A exon
GTATGTCTGATATTTTATTTCTCTTTTGGTGACTCATTTGTCTGCATGTGTTCATGAAACAACCAAACACCTGGCCAAATAGAGAGTCACATCTGTCCAGGATAAACAATGGCTGAATCTGCTATTTGTGAAAGAGAATGGTAAGATTCTGGCCACTCAGGCAAAAATGAGGGAGGGCCACAAGGGGGGTTGAGGGACTGGGCTAGGAAATTCCAAGACTGGAAACAGGCCAGCAAATTCCAAGAAAGGGATTGATGACTTTAAAGAAGAATGAAAAATAATGAGAAGACTCAGGGAGAGATGTGATGGGATCATTGTTTTAGGTATGGAAAAATATTAAAGGGTTTGGCCATTTAAAAGCATTCTAGTTAGAAAAGTTTGGGGCTCAGCATGCTGATTCACGCTAGTTGAATGCTCAGTGTGTCTTCTCTACACTTCAGTGAGTTTAAGAGTACACATCTAGGTTTCCTTGGAGGCACTGTGCCAAGACATGATATTCCCTGAGTTAATATTACTACAACAAATGAATTCAGCTCATCTTTAGGATGGCAGGATTTTGTTGATTCTCTTTCAGGTAACAAAATTCCACTTTGGGAAAATTTTAAAGATAACTTTTAGGCCTATGGAATCTTTTTTTTTTTTTTTTCTTATTTGCAG
Seq C2 exon
CCGTTTTAGAAGAGGAAACTAACAAACATGATACCCACATTAATATTCATAAAGCACAGCTGAGTAAAAATGAAGAGCGATTTAAACTGCTGGAGGGTACTTGCTATAATGGAAAGCTCATTTGGAAGGTGACAGATTACAAGATGAAGAAGAGAGAGGCGGTGGATGGGCACACAGTGTCCATCTTCAGCCAGTCCTTCTACACCAGCCGCTGTGGCTACCGGCTCTGTGCTAGAGCATACCTGAATGGGGATGGGTCAGGGAGGGGGTCACACCTGTCCCTATACTTTGTGGTCATGCGAGGAGAGTTTGACTCACTGTTGCAGTGGCCATTCAGGCAGAGGGTGACCCTGATGCTTCTGGACCAGAGTGGCAAAAAGAACATTATGGAGACCTTCAAACCTGACCCCAATAGCAGCAGCTTTAAAAGACCTGATGGGGAGATGAACATTGCATCTGGCTGTCCCCGCTTTGTGGCTCATTCTGTTTTGGAGAATGCCAAGAACGCCTACATTAAAGATGACACTCTGTTCTTGAAAGTGGCCGTGGACTTAACTGACCTGGAGGATCTCTAGTCACTGTTATGGGGTGATAAGAGGACTTCTTGGGGCCAGAACTGTGGAGGAGAGCACATTTGATTATCATATTGACCTGGATTTAGACTCAAAGCACATTTGTATTTGCCTTTTTCCTTAACGTTTGAAGTCAGTTTAAAACTTCTGAAGTGCTGTCTTTTTACATTTTACTCTGTCCCAGTTTGAAACTTAAAACTCTTAGAATATTCTCTTATTATTTATATTTTTATATTTCTTGAAAGATGGTAAGTTTCTTGAAGTTTTTGGGGCGTTTCTCTTTTACTGGTGCTTAGCGCAGTGTCTCGGGCACTCTAAATATTGAGTGTTATGGAGGACACAGAGGTAGCAGAATCCCAGTTGAAAATGTTTTGATATTTTATTGTTTGGCCTATTGATTCTAGACCTGGCCTTAAGTCTGCAAAAGCCATCTTTATAAGGTAGGCTGTTCCAGTTAAGTAGTGGGTGATGTAGTTACAAAGATAATATGCTCAGTTTGGACCTTTTTTTCAGTTAAATGCTAAATATATGAAAATTACTATACCTCTAAGTATTTTCATGAAATTCACCAGCAGTTTGCAAGCACAGTTTTGCAAGGCTGCATAAGAACTGGTGAATGGGGTAAGCATTTTCATTCTTCCTGCTGAAGTAAAGCAGAAAGTACTGCATAGTATATGAGATATAGCCAGCTAGCTAAAGTTCAGATTTTGTTAGGTTCAACCCTATGAAAAAAACTATTTTCATAGGTCAAAAATGGTAAAAAATTAGCAGTTTCATAAGATTCAACCAAATAAATATATATATACACACACACATACATATACACCTATATATGTGTGTATACAAACAGTTCGAATGTATTTTGGTGACAGTAATAAATCAATGTGAGGATGGATAGAATTTAGTATATGATAGAGAAAATGTCATAAATGGATAAAAGGAATTTACAACTTGAGGAGAAAACCTTTACAATTTCCTATGGGTGTCAGAAGTACTCTCAGCGAAAACTGATGGCTAAAACAGTATCTACTATTCTCTGATAACTTTTTTTTTGAGACAGAGTTTCATTGTCACCCAGGCTGGAGTACAGTGGCATGATCTCAGCTCACTGCAAACTCTGCCTCCCGAATTCAAGTGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGATTACAGGCGCCCGTCACCACACCCAGGTAATTTTTGTATTTTTAGTAGAGACGGAGTTTTGCCATGTTGGCCAAGCTGATCTCAAACTCCTGACCTCAAGTGATCTGCCCGCCTCGGCCTCCCAAAGTGCTGAGATTACAGGCATGACCCACCGCGTCAAGCCTCTGACAACTATTGAATTTGTAAGCTGCTATGCAAATGGGCATTTATATAAACTTGTGATGTTTCTTGTCAGAATTCTGAGTACTCTGTGAAGAACAGAAATGATCATATTCTTATGCATCTATCTGTATGGGTCTGAAGGTGTATATACAAACTGAGATGAGTCCTTATGACTCTTGATAAGCCTGAGTTTAACAACAACAAAAATGCCAAGTTGTCCTGAGCCCTTCTGCGTTGTTATGCCACTTCCCTACTGCTCATATGCACGCTGGCTCCCCTGGGCACGCAAGGATGAGTATGGGCCATGGGCCCCTGTAGAGCTGCTTACCTGGTGATGACCATGCACCTTACAATTTCTGAACAGTTAACCCTATAGAAGCATGCTTTATATGAGTGTCTTCTGGGAAGAGGAACCTTCTTAATCTCTTCTGTGGGATTTTCAAAATGCTAAAGACTCACACTGCAGCAATCATCCCAGATGATTAAATTCAAAGAAATAGGTTCACAACAGGAATATACTGAAGAACTAGAGTGTCACTGCTGGTGAACTGTGGCACGGTTGCTCAACACATCACCTCGGACAAATTCAGGAAGCATTTCTTTAGCCCACAAGTCCAGACCCAGGTGCTCTGTATGTTTGTTTTTAATATTCATCATATCCAAGTTCACTCTGTCTTCCTGAGCAGTGGAAGATCATATTGCTGTAACTTCTTTTAAGTAGTTGATGTGGAAAACATTTTAAAGTGAATTTGTCAAAATGCTGGTTTTGTGTTTTATCCAACTTTTGTGCATATATATAAAGTATGTCATGGCATGGTTTGCTTAGGAGTTCAGAGTTCCTTCATCATCGAAATAGTGATTAAGTGATCCCAGAACAAGGAATACTAGAGTAAAAAGCACCTCTTTTTCACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000082512-TRAF5:NM_004619:10
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.089
Domain overlap (PFAM):
C1:
PF059116=DUF869=FE(21.5=100),PF100464=BLOC1_2=PD(31.6=54.4)
A:
NA
C2:
PF059116=DUF869=PD(20.3=27.6),PF0091721=MATH=WD(100=74.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTGGCTAGAAGCTCAAGTGCA
R:
TGGTGTAGAAGGACTGGCTGA
Band lengths:
347-1004
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)