GgaINT1028422 @ galGal4
Intron Retention
Gene
ENSGALG00000009864 | TRAF-5
Description
TNF receptor-associated factor 5 [Source:RefSeq peptide;Acc:NP_989550]
Coordinates
chr3:21612005-21612561:-
Coord C1 exon
chr3:21612397-21612561
Coord A exon
chr3:21612083-21612396
Coord C2 exon
chr3:21612005-21612082
Length
314 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGG
5' ss Score
10.51
3' ss Seq
TTGTTTTTCTTTTTCCCCAGAAT
3' ss Score
11.12
Exon sequences
Seq C1 exon
GAACATCTTCAGCAGTGTTTGTTTGAAAGCGTGCAATGCACTAATGATGGATGTTGTGATCAAATCCTTCGGAAAGATTTGAAAGACCATTTGAGTCAGCACTGTAAATTTCGAGAGGAAATGTGTCAGTACTGTAATAAATATGTGGTGTTAATTAACATAAAG
Seq A exon
GTAAGGTTATAAAACATTCCCTGGAATCCATCCATACATTTGCCTCTTAATATTGCTGAGTGAAACGTTTCCAGCACTGCAGTGGGATTTTACCACTCAAGAAACAAAACTTGGCTGAGTAGCCGAAGGAGAAAGCCTAATAAAAATGAGCATGCTTTAACTAATACCAGTTACTCTTGCTCTCTTAAAAACATGATGTGGGGCTTGCACGTGTATGTTTATGATTACTTTTTGCATGCCAGAATTAATAACTTCTTCTACGTATACTGCTTTACAAAAATGCAAACCATTGCCTTGTTTTTCTTTTTCCCCAG
Seq C2 exon
AATCATGAGGAAAACGACTGTCCTGATTATCCCATGCCTTGTCTCCAAAACTGTTCACAGATAATTCTGAAAAAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009864:ENSGALT00000016038:6
Average complexity
IR
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:
NO
A:
NA
C2:
PF0217613=zf-TRAF=PU(40.7=92.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAACATCTTCAGCAGTGTTTGT
R:
ATTATCTGTGAACAGTTTTGGAGACA
Band lengths:
230-544
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]