BtaINT0152202 @ bosTau6
Intron Retention
Gene
ENSBTAG00000012020 | TRAF5
Description
Bos taurus TNF receptor-associated factor 5 (TRAF5), mRNA. [Source:RefSeq mRNA;Acc:NM_001105340]
Coordinates
chr16:73897157-73898842:-
Coord C1 exon
chr16:73898702-73898842
Coord A exon
chr16:73897326-73898701
Coord C2 exon
chr16:73897157-73897325
Length
1376 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGA
5' ss Score
9.22
3' ss Seq
GATCTATTTTGTACTGAAAGGTT
3' ss Score
5
Exon sequences
Seq C1 exon
ATTTCTGACTTATATAAGAGCCTAGAACAAAAAGAAAGCAAAATCCAGCAGCTAGCAGAAATGGTAAAGAAATTCGAAAAGGAGTTCAAGCAATTTGCACAGTTGTTTGGCAAAAATGGAAGCTTCCTCTCAAATATGCAG
Seq A exon
GTGAGAAATGGCCTTTCTATTCATAACCCAGATTTAACCTCACAGCCAGTTAGCTTTTTAACTAACTTTTTAAATGGAGAAACTAACTTTTTAAATGGAGATAATTCCAAAGGTGCAAAGCTAAGACAGTACAAAGAACACCTGTGTGTTCCGCACCCAGATTCACTCGTCGACAGTGTTCTGTCCCGTTTGCTTCCTTCATCCTGTCTCCCCTGCCTCATCCCAACCCTGTCCTTAGCCCCCATCCTGTCCCTGTCTCTCTCTCTTTGTGGGTGTTCTTTCTGAACCCTTTGAGAGTAAGCCGCCTATTATAGCCCTTTACCCCTACACGCTTCGCAATGTATTTCCTAAGAATAGAGATCTTTTACATAACCCAGTGCACTTAGCCATGCCAGTACACGTTTGCACTGGTACAGTACTTTTACACAATTTATGAGGGTTGTCACTATTGACCCAATATTTGTCACTTGACTTCAGATTTATTGAGCACATCTGTAGTTCTGCATTTTGCAGTCAACAAAGTAAAACTATTAATTCCTTTGGGAAGAAAATGCTTTACACATTACTAAAATAGAGCAAAAATTACTTTGTAAATCATGACTGTTAAGTAACCATAAACAGATTTCTAAAGAATAATGTCTTTATTGTGATTTTAAAATTTATAGTGCAAAATATTTCATAATGTGATATGGGCAATCTTTTTGAGGATTATACCAGAAAATGTAGGCCATGTCATTTCCATACTTTGTCCGCATACTGTATGGATGTGTGTGTGTTTGCGTATAGCAAAAAGGAAATCCATCAATTGTTGTTATCTTAATTCTGACCTTTTTCTAACACAAAAACCAGTCAAGAGTGAAGACACTGAGGGCGGGAGAAATATAGTTTTGTTTAATCCCTTCCATCTAAAGAGAGCAACTAAGTGTTCAGGCCTTATCTTGGGGCACTGAGTACCACCTGCCGTGCTCAGACCAGAACAGATGGGCCTTCTTCCAGCACATTCTCTGCCCTCTCGCAGAGCGGGAGTGAATCAGAAGCGTTGTGACAGAGAAGGAAGTGATAAGGCAAGAGGACAGACAGGGAGAACATAAATACAAAGATAGGCTAAAGAACCAAGAGGGGAAAATCCAAGGGAGAAGTAAGACTCAGGTGAAGAACAGTTCAAAGATTTGAAACAGGAGCCAAGATACTGTAGAGCGGGGAGGAAGGTATTAGGTGATTCATCTCTCTGACATCCTATCCTCTCTCTTCTGAACCGTGCATTTTTTTCACTGCATTAATTGGTTAATTCAAGGTGAAATGTTTGAGATGAAAAAATGTGATCTCAAAGAATCATTCATGTTTTTTTGACGTGTTGATCTATTTTGTACTGAAAG
Seq C2 exon
GTTCTTGCCAGTCACATTGACAAGTCTGCTTGGCTAGAAGTTCAGGTGCGTCAGTTACTACAAATGGCTAACCAGCAACAGAGTAAATTTGATCTGAAGCCTTTGGTGGAAGCAATTGATACAGTGAAACAGAAAATCACCCTGCTGGAAACCAATGACCAAAGACTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000012020:ENSBTAT00000015940:9
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:
PF059116=DUF869=FE(18.5=100)
A:
NA
C2:
PF059116=DUF869=FE(22.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping 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:
AAGAGCCTAGAACAAAAAGAAAGCA
R:
TAGTCTTTGGTCATTGGTTTCCAGC
Band lengths:
294-1670
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development