BtaINT0001477 @ bosTau6
Intron Retention
Description
Bos taurus major histocompatibility complex, class I, A-like (LOC616942), mRNA. [Source:RefSeq mRNA;Acc:NM_001206459]
Coordinates
chr23:27844712-27845210:+
Coord C1 exon
chr23:27844712-27844987
Coord A exon
chr23:27844988-27845096
Coord C2 exon
chr23:27845097-27845210
Length
109 bp
Sequences
Splice sites
5' ss Seq
GGGGTAAAG
5' ss Score
3.53
3' ss Seq
CTCTTCCTTTTCCTCCACAGAAC
3' ss Score
12.72
Exon sequences
Seq C1 exon
ACCCTCCAAAGACACATGTGACCTGTCACCCCATCTCTGGCCGTGAGGTCACCCTGAGGTGCTGGGCCCTGGGCTTCTACCCTGAGGAGATCTTACTGACCTGGCAGCGTGACGGGGAGGACCAGACCCAGGACATGGAGCTTGTGGAGACCAGGCCTTCAGGGGATGGAACCTTCCAGAAGTGGGCGGCCCTGGTGGTGCCTTCTGGAGAGGAGCAGAGACACACATGCCGTGTGCAGCATGAGGGACTTCAGGAGCCCCGCACCCTGAGATGGG
Seq A exon
GTAAAGATGGGGTCGGAATGGAGCTTTTCTCAGATAAAGCAGGAGCCCTTCAGGACTCAAAAGTCAGGACTCAAGCCTGAGGTCAGGGCCTCTTCCTTTTCCTCCACAG
Seq C2 exon
AACCTCCTGAGACCTCCTTCCTCACCATGGGCATCATTGTTGGCCTGGTTCTCCTTGTGGTAGCTGTGGTGGCTGTGGTGACTGGAGCTGTGATTTGGAGGAAGAAGCGCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000007075:ENSBTAT00000009299:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.355 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0765410=C1-set=WD(100=93.5)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm10)
No conservation detected
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GATCTTACTGACCTGGCAGCG
R:
ACCACAGCTACCACAAGGAGA
Band lengths:
258-367
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]