HsaINT0171754 @ hg19
Intron Retention
Gene
ENSG00000082512 | TRAF5
Description
TNF receptor-associated factor 5 [Source:HGNC Symbol;Acc:12035]
Coordinates
chr1:211533254-211534121:+
Coord C1 exon
chr1:211533254-211533418
Coord A exon
chr1:211533419-211534043
Coord C2 exon
chr1:211534044-211534121
Length
625 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAAA
5' ss Score
5.07
3' ss Seq
TTGCACTTTCTCTATTTCAGAAT
3' ss Score
11.03
Exon sequences
Seq C1 exon
GATCACCTTCAGCAGTGCTTATTTCAACCTGTGCAGTGTTCTAATGAGAAGTGCCGGGAGCCAGTCCTACGGAAAGACCTGAAAGAGCATTTGAGTGCATCCTGTCAGTTTCGAAAGGAAAAATGCCTTTATTGCAAAAAGGATGTGGTAGTCATCAATCTACAG
Seq A exon
GTGAAAAACAACACATACAACAGTCATCTTTATGGAGCTAAATTATGCCTGAGTGGTCACAGTGAATCAGGTGGAATGCCAGAAGAACATTCCTGCATTTATTTTTGTACAGAATTAGGTCTAAAGAATTTGCTTTTTGGAGAGAAGTTCTGTGAAAAGCTTAAAACCTTCTTGTTGGTAGCACTCCATTTATTATTGGCAAAAATATTATTTGAACACATGCTGTGTATGTGTAATGAATGCTGGGTGCTGAGTCACAAGGAGGTGACAATAATGTCTACTCTCTGAATTCTGCAGTGTAGCTGGGGAGGCAGGATGCAGGCATAAAAAGAAAGCATGGGTACCTTTTACATGTCCCGAAGGAGCTATGCTGGCAGTTCCCCAATCTACCTTCTTTGAATCCTGTGTTCTATGACTTTCTTTTGGAATAATTGGAAAATTTAATATTTTAATTAAGTTCATTTACACCTAGAAAGTGGACATCTTTAATCCTTTTTTGGAATTAGGCAATAACTTCCTGTAGAGAGTAAGCCACGTGACATATAATCCCCAAAGAGACACAGGTGTAATCACTGTGAGGCCATGAAAGACAACCCTTTGTTTTATTGCACTTTCTCTATTTCAG
Seq C2 exon
AATCATGAGGAAAACTTGTGTCCTGAATACCCAGTATTTTGTCCCAACAATTGTGCGAAGATTATTCTAAAAACTGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000082512-TRAF5:NM_004619:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF059116=DUF869=PU(8.0=38.2)
A:
NA
C2:
PF0217613=zf-TRAF=PU(40.7=92.3),PF059116=DUF869=FE(9.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GATCACCTTCAGCAGTGCTTA
R:
TCAGTTTTTAGAATAATCTTCGCACA
Band lengths:
242-867
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- 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)