BtaINT0152198 @ bosTau6
Intron Retention
Gene
ENSBTAG00000012020 | TRAF5
Description
Bos taurus TNF receptor-associated factor 5 (TRAF5), mRNA. [Source:RefSeq mRNA;Acc:NM_001105340]
Coordinates
chr16:73905799-73906658:-
Coord C1 exon
chr16:73906494-73906658
Coord A exon
chr16:73905877-73906493
Coord C2 exon
chr16:73905799-73905876
Length
617 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAA
5' ss Score
8.59
3' ss Seq
GCACCCTTTCATTGCTTCAGAAT
3' ss Score
7.6
Exon sequences
Seq C1 exon
GACCACCTTCAGCACTGCCTGTTCCAGCCTGTGCAGTGTTCTAATGAAAACTGTCGGGAGCCAGTCCTTCGCAAAGATCTGAAAGAGCATCTGAGCGCATACTGCCAGTTTCGAGAGGAAAAATGCCTTTATTGCAAAAAGGATGTGGTAGTCATCAATCTACAG
Seq A exon
GTAAAAAAAAAAAGGCATCTTTATGGGACTGAATTCTGCCTGAGTGGTCACAGTGAATCAGATGGGGTACCAGAAGCACTTTTCTGAATTTATTTTTGTGCAGAAAGAGGCCTAAAGAATAACTTATCTGAGGGTTCTATAAAAAGCTGAAAGCCTTCTTGGTAGGTCTCTTTTCATGTATCATTGGCAAAAATGCTGTTTGATTACCTGCTGAGTGTGAGTGGGCCAAGTGCACACTAGTAGCTGAGTCACAAGGAGGGGACCACACTCTTTGTCCTCAGGATGCTCTGACAATTGGCGAGGCAGGATGCAGGCGTAAGAAGAAAGTGTGGGTACCTTTTACATGTGCCAAAGAAGCCATGCCAGTGACGTGCATCATCTGTCCTCTGCCGGCCCCATGGCCTCTGCCCTTCTTTGGAATAATTGGAAAACTGAACTCGTTTATACTGAGAAAACAACCGTCAGGAACCTTTTTGCTGCTAGGCTGTACCTTCTTGTAGAGGATGAGCCACACTGCATAGGTCCCCAAGGGGTTATATGTGCACACACTCTGAGGGCATACAGGGAGCCTTTGGAAGCCAGGTTGGCTTTATTTCAGCACCCTTTCATTGCTTCAG
Seq C2 exon
AATCACGAGGAAAACCTGTGTCCTGACTACCCAGTATCTTGTCCCAACAAGTGTTTGCAGACCATTCCAAGAACTGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000012020:ENSBTAT00000015940:5
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=PU(1.6=7.3)
A:
NA
C2:
PF059116=DUF869=FE(10.1=100),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:
CACCTTCAGCACTGCCTGTTC
R:
TCAGTTCTTGGAATGGTCTGCA
Band lengths:
239-856
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development