HsaINT0171751 @ hg19
Intron Retention
Gene
ENSG00000082512 | TRAF5
Description
TNF receptor-associated factor 5 [Source:HGNC Symbol;Acc:12035]
Coordinates
chr1:211526581-211527809:+
Coord C1 exon
chr1:211526581-211526799
Coord A exon
chr1:211526800-211527751
Coord C2 exon
chr1:211527752-211527809
Length
952 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGT
5' ss Score
10.03
3' ss Seq
ATTTTAATTTTTTTCTCCAGAGA
3' ss Score
9.31
Exon sequences
Seq C1 exon
AATGGCTTATTCAGAAGAGCATAAAGGTATGCCCTGTGGTTTCATCCGCCAGAATTCCGGCAACTCCATTTCCTTGGACTTTGAGCCCAGTATAGAGTACCAGTTTGTGGAGCGGTTGGAAGAGCGCTACAAATGTGCCTTCTGCCACTCGGTGCTTCACAACCCCCACCAGACAGGATGTGGGCACCGCTTCTGCCAGCACTGCATCCTGTCCCTGAG
Seq A exon
GTGAGTGGGCAGGGCCTGCAACTCTGGCCATGGCAGTCCTAGCATCCAGGTGGCAACTGTGGCCACTCAACTGTTTTCATGGGTTTTGGAGTTGTTTTACTTGGCCACAGAACCATGACTGTAAGGAAGGACTCTCCCAGATCCCCTCTGTGAGGGCCTGAAGAATAATCATTTTTTGGTCACTAATTTACAGATATTTACCTTTTCTTAAAATTCAGACTGTACCTGCTTTGCATGGGACAGCAGACCTAGACACACACTCCATCATGGGAGCTGGCTGTGGAGAAGGGCTTGAATCTCACAATGTCTGTGTTGTAGTCACCCCAATCTTCCCTTGCCTTGAGGCAGAGGTGCTGTGGCACCTAGAAGGGACCTTGCTGCCATGGATGCTGTCCACTCCTGGGCAGCTGTAAGACCTGGGTCATACTGTGTTGAGGGAGGATACCAGGAGAGATGTGGAAGCAGGTACACTTTGGGGGGTTATATAGGAAGCAAGGCAGTCATTTTACCCTGCCAAGCTTTGAAAGGGGGTTATTACAGCACATCCTCATTCCCTCATGTGTTTGTGCCTTCAGCACCTGTGTGTTCTGTGCTGTCATGCTGAAGAGCTACAATGTGGAACAGGACCCCATGTCTGCCCTCTAGAATGTCCCAGTCTAGAGGAGACAAATGTGGCACAGCGTGATAAACAAAGGACAGGGGGCATTCAGCTCTGTCCAGGGACTCACTGACTGCATCCCAGAGGTTGCATGAAGTTTTTCAGGCAAACTGAAAGAACAGGAAGGTGCTGAAGGAGGGGTACAGGAGGCCCCTTCTGGGTAGAGGGAACAGCATGTGCAGACAGGGACCAGCCTGCCCAGGGCTAGAGCATGGCTGGAGCCCTGGGGCTGGTCTTGGAAATGCTGTTGAGGTAAACAACTAACTCTGGCTCCATTTTAATTTTTTTCTCCAG
Seq C2 exon
AGAATTAAACACAGTGCCAATCTGCCCTGTAGATAAAGAGGTCATCAAATCTCAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000082512-TRAF5:NM_004619:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0009720=zf-C3HC4=PU(71.8=38.4)
A:
NA
C2:
PF0009720=zf-C3HC4=PD(25.6=50.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGCTTATTCAGAAGAGCATAAAGGT
R:
CTCCTGAGATTTGATGACCTCTT
Band lengths:
275-1227
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)