GgaINT1028424 @ galGal4
Intron Retention
Gene
ENSGALG00000009864 | TRAF-5
Description
TNF receptor-associated factor 5 [Source:RefSeq peptide;Acc:NP_989550]
Coordinates
chr3:21611204-21611634:-
Coord C1 exon
chr3:21611560-21611634
Coord A exon
chr3:21611297-21611559
Coord C2 exon
chr3:21611204-21611296
Length
263 bp
Sequences
Splice sites
5' ss Seq
AAGGTAACG
5' ss Score
10.19
3' ss Seq
TCCCTTTCTGCCTCACTAAGGTG
3' ss Score
6.51
Exon sequences
Seq C1 exon
ATTGAAAAGCATCATACTGTGTGTCCTGAGACTGAAGTGGACTGCCCATATAAACAGTATGGCTGTCTTATAAAG
Seq A exon
GTAACGTTTGATAGATCATTGCTTGTACTAGGAATTTGTCTCCCAAACCAATCAGAGTAGTTAATTAAGATAACCATTTTTAGTTCTTTTACAACCATTTCTAGTAAGATGCTACAGCAGAGAACCAGGACTGTTGTTCCCTCACTTCCAATGCACAGAGGGGACATTTTAAATCCTGACATCAGTAAATTTTTTACCCACCAGCTTCAATAATCTGTGTATCTGATCGTTTTGTTCTTTTGCTCCCTTTCTGCCTCACTAAG
Seq C2 exon
GTGAAAAGAGGGAAGCTTGCTGAACATGAAAACGGTGCCCTGCGGGAACACATGCTGCAGATTTTGGACAAGAATTCTAGATTGGAAGAACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009864:ENSGALT00000016038:8
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:
PF0217613=zf-TRAF=FE(40.7=100)
A:
NA
C2:
PF0217613=zf-TRAF=PD(13.6=25.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGAAAAGCATCATACTGTGTGTCCT
R:
GTTCTTCCAATCTAGAATTCTTGTCC
Band lengths:
164-427
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]