DreINT0167118 @ danRer10
Intron Retention
Gene
ENSDARG00000030173 | traf2a
Description
Tnf receptor-associated factor 2a [Source:ZFIN;Acc:ZDB-GENE-071120-2]
Coordinates
chr5:28166841-28167420:-
Coord C1 exon
chr5:28167233-28167420
Coord A exon
chr5:28166920-28167232
Coord C2 exon
chr5:28166841-28166919
Length
313 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGC
5' ss Score
9.85
3' ss Seq
GCTCTTCTTTTCTCTCGCAGCTC
3' ss Score
10.8
Exon sequences
Seq C1 exon
ATGGCTGCACAGGAACCCTCACCACCATCTTCATTAGAAGGCAACAAACCTGGCTTTCCCAAGAAAATACTCGCCAACAAGCTGGAGGACAAGCATCTGTGCAATATCTGCCTGAAAATCCTTAGGAGACCGTTTCAGGCGCAGTGCGGACATCGTTTCTGTTCGTATTGTTTTAATAAAGCAGTGAG
Seq A exon
GTAAGCGGCATTCAGTCCTGATGGCCCACCTGACACGACAACTACAAAAGATGAACACGACCTGTCAGGCCTCCCGTGCCATTTTACAACATGTTTTATGGGTTATACGAGCAGTAAAACTATGTTTTATGTCGGGGAACATAAATAAATGCAGGCTGTCAGGTTGTGTTCGGCTTCTTGTTTAGCTGTAAACTACAATAGCCAGACTGTTGTCAGGATGAACACTTCTCTTATTGTATGTGTCTTTTGTATTTATTAGCGAGTTTGGCTTTTTGTGCTTGTCTATAATGAAAGCTCTTCTTTTCTCTCGCAG
Seq C2 exon
CTCCGGACCACAGAAATGCAGTGCCTGCATAAAAGAGGACATATTTGAAGAGCCAACATCAATTTTGAAACAGGGCTGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000030173:ENSDART00000158299:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.254 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0009720=zf-C3HC4=PU(74.4=46.0)
A:
NA
C2:
PF0009720=zf-C3HC4=PD(23.1=33.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Human
(hg19)
No conservation detected
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTGCACAGGAACCCTCAC
R:
AGCCCTGTTTCAAAATTGATGTTGG
Band lengths:
262-575
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]