BtaINT0152195 @ bosTau6
Intron Retention
Gene
ENSBTAG00000012020 | TRAF5
Description
Bos taurus TNF receptor-associated factor 5 (TRAF5), mRNA. [Source:RefSeq mRNA;Acc:NM_001105340]
Coordinates
chr16:73911104-73912109:-
Coord C1 exon
chr16:73911891-73912109
Coord A exon
chr16:73911162-73911890
Coord C2 exon
chr16:73911104-73911161
Length
729 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGC
5' ss Score
8.7
3' ss Seq
ATTTTGACTTTTCTTTACAGAGA
3' ss Score
9.12
Exon sequences
Seq C1 exon
GATGGCCTATTTTGAGGAGCAAGGAGGAGTGCCCTGTGGTTTCACCCGCCAGAATTCTGGCAACTCCATCTCCTTGGACTTCGAGCCCGACGCGGAGTACCAGTTTGTGGAGCGGTTGGAAGAGCGCTACAAGTGTGCCTTCTGCCACTCAGTGCTTCACAACCCCCACCAGACGGGCTGTGGGCACCGCTTCTGCCACCAGTGCATCCTGGCCCTGAG
Seq A exon
GTGAGCTGGCGGGGCCTCCGCTCCCGCCAGAAGCGGCCAGCGTGTTCCCGGGAGCGGCCATCTGTGGCCGCTCAACTAAGATCAGGGTTTCGGGAATTGCTGTGGTTGCCCACAGAACCACAAATTTGGAGACGGGCTTTCCCAGGGCCCTTCTCTGAGAGCCTGAGGAGTATAACCTTCATTTTCTTCCCACTATCCTATTGATCGTCACCTTTTCAGACCACACCTGTTTTGCACGCGAGGGCCAACCTCTGTGCACAGTCTACACCGGGAAGGACCTGTCTCCCAAGAGGGTCTTTCTTGTAGGCGCCCTGACCTTCCCCTGCCTTGAGGCAGGGCACAGAGGTGAAGTGTTAGAGGTTAAGTGTGAAACAGGACCCTCTAGAATCTTCTGTTCTAGTGGAGGAGACAGGTGGTGGTACAGTGTGATAGCATAGGACCGCCAAGGGAACATTGGCAGAGAACATTTGACTCTGTCTGCGGGACTCCCTCTTGGACTCACATCCTGGAGGATGAATGGGACTTTCAGGACTTTCACTGAGGAGGTGCTGAAATTGGGGTGCCAGAGGGCGCCTTCTGGAAAGAGGGAACAGCATGAGTAAAGATGGGGCCTGGCCTGCTCAGGGGGGACTTCAAGGGGTCAAGTGTGGCTGGAGTGCTGGGGCTGCTCTTAGAAAGGTTGTTGAGGTCAACCCTTAACTCTGGCTTCATTTTGACTTTTCTTTACAG
Seq C2 exon
AGAATTGGACACAGTCCCACTCTGCCCTGTAGATAAGGAGGTGATCAAATCTCAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000012020:ENSBTAT00000015940:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0009720=zf-C3HC4=PU(71.8=38.4)
A:
NA
C2:
PF0009720=zf-C3HC4=PD(25.6=50.0)
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:
TGGCCTATTTTGAGGAGCAAGG
R:
CTCCTGAGATTTGATCACCTCCT
Band lengths:
275-1004
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development