BtaINT0072782 @ bosTau6
Intron Retention
Gene
ENSBTAG00000020772 | HMHA1
Description
histocompatibility (minor) HA-1 [Source:HGNC Symbol;Acc:HGNC:17102]
Coordinates
chr7:45187624-45188042:+
Coord C1 exon
chr7:45187624-45187761
Coord A exon
chr7:45187762-45187851
Coord C2 exon
chr7:45187852-45188042
Length
90 bp
Sequences
Splice sites
5' ss Seq
TCGGTGCGC
5' ss Score
7.09
3' ss Seq
CACCTCCCGCCCGTCCACAGGCC
3' ss Score
10.25
Exon sequences
Seq C1 exon
GCGGAGGAAGCAATGGCCACCTACCGTACATGCGTGGCCGATGCTAAGACACAGAAGCAGGAGCTGGAGGATACCAAGGTGACGGCACTACGGCAGATCCAGGAGGTCATCCGGCAGAGTGACCAGACCATCAAGTCG
Seq A exon
GTGCGCACTGGGGCTCCCCTGGAGAGGTGGGAGGAGCACCTACCTGTCAGGTGCCAGGACCACTAGCGCTCACCTCCCGCCCGTCCACAG
Seq C2 exon
GCCACCATCTCATATTACCAGATGATGCACACGCAGACGGCCCCACTGCCCGTGCACTTCCACATGCTGTATGAGAGCAGCAAGCTGTACGACCCAGGCCAGCAGTACGCTTCCCATGTGCGCCAGCTGCAGCGCGGCGAGGAGCCTGATGTGCACTACGACTTCGAGCCCCACGTGTCCGCCAGTGCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020772:ENSBTAT00000027682:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.804 A=NA C2=0.469
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGGCCGATGCTAAGACACAG
R:
TACAGCATGTGGAAGTGCACG
Band lengths:
176-266
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]