BtaINT0072784 @ bosTau6
Intron Retention
Gene
ENSBTAG00000020772 | HMHA1
Description
histocompatibility (minor) HA-1 [Source:HGNC Symbol;Acc:HGNC:17102]
Coordinates
chr7:45188161-45188445:+
Coord C1 exon
chr7:45188161-45188285
Coord A exon
chr7:45188286-45188361
Coord C2 exon
chr7:45188362-45188445
Length
76 bp
Sequences
Splice sites
5' ss Seq
GGGGTGAGT
5' ss Score
7.93
3' ss Seq
TGGGGATACTTCTTTCACAGGTG
3' ss Score
6.15
Exon sequences
Seq C1 exon
GTCCCCAGTCCTGCGTGCTCGGAAAAGCAGCTTCAATGTCAGCGATGCTGTGGGGGCAGAGGCTGCCAGTAGCCCCCCGGAGGACGGCGGGCCCAGCCAGGGAGAGATTGCCAAGGAGCGCAGGG
Seq A exon
GTGAGTGCCAAGAGGGGGCGGACGCAGCCCCCTTGCAGCCCCCCTCAGACCTTCACTGGGGATACTTCTTTCACAG
Seq C2 exon
GTGGGCGGGGCCACCAGGTGCACAAGTCGTGGCCCATCTCCATCTCCGATTCGGAGGCCAGTCTGGACCCCAGCCCTGGCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020772:ENSBTAT00000027682:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.651 A=NA C2=1.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGCTCGGAAAAGCAGCTTCAA
R:
TCCAGACTGGCCTCCGAATC
Band lengths:
177-253
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]