HsaINT0171690 @ hg19
Intron Retention
Gene
ENSG00000131323 | TRAF3
Description
TNF receptor-associated factor 3 [Source:HGNC Symbol;Acc:12033]
Coordinates
chr14:103369592-103372628:+
Coord C1 exon
chr14:103369592-103369766
Coord A exon
chr14:103369767-103371549
Coord C2 exon
chr14:103371550-103372628
Length
1783 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
ACCCTCCTCACCTGTGGCAGGCC
3' ss Score
6.14
Exon sequences
Seq C1 exon
CGAGTGATAGACAGCCAAGCAGAGAAACTGAAGGAGCTTGACAAGGAGATCCGGCCCTTCCGGCAGAACTGGGAGGAAGCAGACAGCATGAAGAGCAGCGTGGAGTCCCTCCAGAACCGCGTGACCGAGCTGGAGAGCGTGGACAAGAGCGCGGGGCAAGTGGCTCGGAACACAG
Seq A exon
GTGAGGCAGGGGCCGGGGCCGGGCCAGCAGTGTGCATCTGGGCCCCGGGCGAGTGCTGGGGCGGGGTCCGTGGGATGAGGGCTATGTTAGGTACATGTGCCTTAGGACAGTTTTTTCTAATTATGGGTAACACGCAGAGGTGTGATGACTTTCCTACTGAAAGTCCCCCAGCAAAGACAAACGTTTCCCGCGCAGGCTTGTCCCCTCCGTGTGAGGCCCTACATGGTGTAGAAAGTAGGGGCAGCTGCAGCCACGGGAAGCTGCAAAGCCCTCCTGGGAGAGACTGGCCGCAGGGTGACCCACAGGACAGGCCCAAGCGCAGATGGCAGAGGCCAGGACCTGCTGGTCGGGGCGCCCCAGACCCCACTCCTAAGGGCCAGGGGGCAGCAGTCCCACCGCGCTCTGCCAGCATGTTTCTGATCCACAAGCAGATGTGGGCCTATGGCTTTGGGGACTGAAAGAGTATTGGGAATATTTACATGAGGAGGATTAATGGCAGAAAGGAACACAGATTACCGGTGTGTGTGTGGGGCCGGATGAAGCAGGCAGAGAATGAGGTTGGAGGAGAGGGGAGCAGCTTCGCCTCCAAGAGAGCAGAGGCCACCTGTGGGTGCTGAGGCCGGAGGGAGGAGTGGGGAGAGCACAGCTGTCTCCTGCTCCCAGGAGCTCCCACCAGCGGGCTTCCCAGGAAGCCACAGTGGAGCACTCTGTCTTGGACCCTGCAGTGAGGTGTCCTTTGACACACAGGCAGGTCAACCGCCCAGGACATCCCCTGTCAGCAGTCTGTGCCTAGTAATGTGTCCAGACAGACAGGGCTGTGGGCATGAGAGCTGTGGTAGAACTGGGGCAGGGACCTGGGCTCTTCCCTGGGAGGCGGTGGCCTCAGGACATCTTCTACACAGTTTTGCTGGTGTTACCCCCAGAAACCACAGTGATTTTTATATTGTTGCTTCAGATGCTGGTATGACTGGGCATGGTGGTGTGGCCTATAGTCCCAGTGCTTTGGGAGGCTGAGGCAGGAGGATTACTTAAGCTCAGGAGTTTGATGCCAGCCTGAGCAACAGAGCAAGACCTTGCCTCTTTAAAAATTAAAAAATGAGGCCGGGTGCAGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGTGGGCAGATCACGAGGTCAGGAGATTGAGATCATCCTGGCTAACACGGTGAAACCCCATCTCTAGTAAAAATACAAAAAGTTAGCCGGGCATGGTGGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGTGTGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATTGTGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCATCTCAAAAAAAAAAAAAAAAAAAGAGCCAGGCACGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGATCGAGGCAGGTGGATCACCTGAGGTCAGAAGTTCGAGACCAGCCTGGCCAACATGGCGAAACCCTGTCCCTACTAAAAATACAAAAATTAGCCAGGCGTGGTGGCAGGCACCTCTAATCCCAGCTGCTCAGGAGGCTGAGACAGGAGAATCGCTTGAACCTGGGAGGCAGAGGTTGCAGTCAGCTGAGATGGTGCCACTGCACTCCAGTCTGGGCAACAGAGCGAGACTCCGTCTCAAAAAAATGAAATAAAATAACGAGTGCTGGTGCAGCTTTGCTTTCCTAACCTCTCTGACGTTCACCTGTCTCATTCACCAAACCCTCCTCACCTGTGGCAG
Seq C2 exon
GCCTGCTGGAGTCCCAGCTGAGCCGGCATGACCAGATGCTGAGTGTGCACGACATCCGCCTAGCCGACATGGACCTGCGCTTCCAGGTCCTGGAGACCGCCAGCTACAATGGAGTGCTCATCTGGAAGATTCGCGACTACAAGCGGCGGAAGCAGGAGGCCGTCATGGGGAAGACCCTGTCCCTTTACAGCCAGCCTTTCTACACTGGTTACTTTGGCTATAAGATGTGTGCCAGGGTCTACCTGAACGGGGACGGGATGGGGAAGGGGACGCACTTGTCGCTGTTTTTTGTCATCATGCGTGGAGAATATGATGCCCTGCTTCCTTGGCCGTTTAAGCAGAAAGTGACACTCATGCTGATGGATCAGGGGTCCTCTCGACGTCATTTGGGAGATGCATTCAAGCCCGACCCCAACAGCAGCAGCTTCAAGAAGCCCACTGGAGAGATGAATATCGCCTCTGGCTGCCCAGTCTTTGTGGCCCAAACTGTTCTAGAAAATGGGACATATATTAAAGATGATACAATTTTTATTAAAGTCATAGTGGATACTTCGGATCTGCCCGATCCCTGATAAGTAGCTGGGGAGGTGGATTTAGCAGAAGGCAACTCCTCTGGGGGATTTGAACCGGTCTGTCTTCACTGAGGTCCTCGCGCTCAGAAAAGGACCTTGTGAGACGGAGGAAGCGGCAGAAGGCGGACGCGTGCCGGCGGGAGGAGCCACGCGTGAGCACACCTGACACGTTTTATAATAGACTAGCCACACTTCACTCTGAAGAATTATTTATCCTTCAACAAGATAAATATTGCTGTCAGAGAAGGTTTTCATTTTCATTTTTAAAGATCTAGTTAATTAAGGTGGAAAACATATATGCTAAACAAAAGAAACATGATTTTTCTTCCTTAAACTTGAACACCAAAAAAACACACACACACACACACGTGGGGATAGCTGGACATGTCAGCATGTTAAGTAAAAGGAGAATTTATGAAATAGTAATGCAATTCTGATATCTTCTTTCTAAAATTCAAGAGTGCAATTTTGTTTCAAATACAGTATATTGTCTATTTTTAAGGCCTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000131323-TRAF3:NM_145725:11
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.034 A=NA C2=0.037
Domain overlap (PFAM):
C1:
PF086146=ATG16=PD(18.5=42.4),PF127182=Tropomyosin_1=FE(39.7=100),PF0149614=V_ATPase_I=FE(31.7=100),PF0205011=FliJ=PD(45.5=76.3),PF101744=Cast=FE(37.7=100),PF100464=BLOC1_2=PD(54.9=84.7),PF138511=GAS=FE(49.6=100)
A:
NA
C2:
PF127182=Tropomyosin_1=PD(16.8=12.6),PF041569=IncA=PD(7.2=7.3),PF0149614=V_ATPase_I=PD(35.0=32.5),PF101744=Cast=PD(9.2=7.3),PF138511=GAS=PD(14.4=8.9),PF0091721=MATH=WD(100=73.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGCTTGACAAGGAGATCCGG
R:
CCAGTGTAGAAAGGCTGGCTG
Band lengths:
350-2133
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)