GgaINT1028418 @ galGal4
Intron Retention
Gene
ENSGALG00000009864 | TRAF-5
Description
TNF receptor-associated factor 5 [Source:RefSeq peptide;Acc:NP_989550]
Coordinates
chr3:21616071-21616946:-
Coord C1 exon
chr3:21616797-21616946
Coord A exon
chr3:21616293-21616796
Coord C2 exon
chr3:21616071-21616292
Length
504 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAA
5' ss Score
8.38
3' ss Seq
CATGTCTGACTTTCCAGTAGGGC
3' ss Score
6.05
Exon sequences
Seq C1 exon
GCGAGGTTAATGTAGCCAAGAACTGACATATAATTAAGTATAATTTTGGAAAAAATGAGATTATAGTCTACCGCTATAAATGAATGATCATCTGGAAAAAGAAGGATGACAAGATAGTGGGCTTTGGGTCTTTTAACACCTAAACTGAAG
Seq A exon
GTAAAATCCCTTTACTCCTGTTTTTATTTTGTGTGTACTCCTGGCCATGAGCCACAAAGCTATCTTGTTTGCGCCAGTGCAGTAAATTTGTGATACTGTGTGGGAGGGTTCCACGTTAAGCACAGACTTTCCTGGCAGACCTCAGGGCCAGTACTTGGCCTCTGCTTTCCCCACGTGTGCTTGCTTTAAATGTTGGTGTTTTTAAACTAACAGTTCCTGCAAGAAATTTGAGAAAAAATTCCCTGTTCTGGGAAATAGTTCTCAAATCCTGATACTCCTTCCAAAGTGTGCTTTAGTGCTTGTCACGTAAGCATCATCTTGGGGTTCTCTGAGCATTCTGTTGTACTTCCATAGTTGATGTCACATTTCCCTCTGAAATCTGTTGGACCCTTCTGCAAGCTGAAACCCTCAAACAGATGGCAGCCCGCTGCAGGCTATAGCAGAACTGAAGTGACTGATGGTGAGCGTTTAATAAGATTCTTCCCATGTCTGACTTTCCAGTAG
Seq C2 exon
GGCTTCCATGGCCTGTGACGAGCTCACTGGTGTCTCGGGCATCTTTACGCGCCAAAACTCTGCTAGTGCTGTTTCTCTGGACTTCGAACCCGACACTGACTACAAGTTTGTGGAAACCTTAGAAGACCGGTACAAGTGTGCCTACTGCCATTCAGTCCTTCACAATCCCCACCAGACAGGATGTGGGCACCGATTTTGCCAGCAGTGCATTCTCACTTTGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009864:ENSGALT00000016038:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.000
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
PF139231=zf-C3HC4_2=PU(70.0=38.9)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Mouse
(mm10)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCGAGGTTAATGTAGCCAAGA
R:
AAAATCGGTGCCCACATCCTG
Band lengths:
347-851
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]