GgaINT1028425 @ galGal4
Intron Retention
Gene
ENSGALG00000009864 | TRAF-5
Description
TNF receptor-associated factor 5 [Source:RefSeq peptide;Acc:NP_989550]
Coordinates
chr3:21610412-21611296:-
Coord C1 exon
chr3:21611204-21611296
Coord A exon
chr3:21610553-21611203
Coord C2 exon
chr3:21610412-21610552
Length
651 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGT
5' ss Score
10.08
3' ss Seq
CTGTACTTTTCCATCTGTAGATA
3' ss Score
10.02
Exon sequences
Seq C1 exon
GTGAAAAGAGGGAAGCTTGCTGAACATGAAAACGGTGCCCTGCGGGAACACATGCTGCAGATTTTGGACAAGAATTCTAGATTGGAAGAACAA
Seq A exon
GTAAGTTGTATTTAATGAACACTCTTCAACAGCTCTTGGCAGCTTGGAAGATTATATGAGATTTTGCATTTGTTGTCTGTAACAGCTCAGCTGCATTCTAAAAAGACTGGTTTTATTGTCCTTGCTTACCTCAGAAGTCAGAATATGCTCTTCTAGTGAAGTCAGGCAATTAGCTGGAAACTTGTCTGTGCTCAGGCATGTGTATTCTCCATCAGGCACAATGGGAGCCTTGTTGCCATCACTTACATCATTTGCTTTTGAACTCTCACAACTGATGCCACGTTTGTGGATAGAGCATTTGAAGGTTTCGGGGGCCAGTCAGATTGCCTTGAAAAGGAGCCTTGGGGTGCTGAAGTCATCCCCTCTGCAGAGGTGGCACAGAGCAGTGCAGAGCCTCCTGCCCACTTCCAAGTTAATACCGTGGCTTATAAAAATCTCACTTTGCAAGCTGGGCAATAACAAGTCAGACTTAAGATGCGGGGACGTCAGTATTTGACAGCGCGTATCCCTGATTTTTGAATTATCCAGCTAAGTTAGCGGTTTTACACTGTAAACTTTTCTGCTTTCTCCTGCACCATAACATGTTTTAATTTAATCCCGGTGCATTTTGGTTGTGCATGGAGCTTTTACTCTGTACTTTTCCATCTGTAG
Seq C2 exon
ATATCTGACCTGTACAAGAGCCTGGAATGTAAAGAGATTAAAATCCAGCAGCTAGCAGAGGCTGTTAAAAAGTGTGAGAAAGAATTCAGACAGTTTACACAACTGTTTGGTAAAAATAGCAATTTGATGGTAAGCACACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009864:ENSGALT00000016038:9
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=PD(13.6=25.8)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAAGAGGGAAGCTTGCTGAACA
R:
CTGTGTGCTTACCATCAAATTGCT
Band lengths:
230-881
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]