BtaINT0072781 @ bosTau6
Intron Retention
Gene
ENSBTAG00000020772 | HMHA1
Description
histocompatibility (minor) HA-1 [Source:HGNC Symbol;Acc:HGNC:17102]
Coordinates
chr7:45187330-45187761:+
Coord C1 exon
chr7:45187330-45187399
Coord A exon
chr7:45187400-45187623
Coord C2 exon
chr7:45187624-45187761
Length
224 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
ACCTACCACCCCCACCCCAGGCG
3' ss Score
6.21
Exon sequences
Seq C1 exon
CGGTGCAGGGGGTGCAGCCTCCAAGACCCTGGACAAGCGTCGTCGCCTGGAGGAGGAGGCCAAGAACAAG
Seq A exon
GTGAGGGCCAGTGATGGAGGGCAAGGCCCATGGTGACAGATCCTCACGCCCTGTACAGAATTGCCCACCTCTGGTCCCTTGTCCAGGCTCTGCCTCCTGGCAGGAATGCCTTCCCATCCTTTTGTACCTAGTTGATTTCTTTGTGGGGCCTGAAGATGCCCTGAGGGCTGAACCGTGGGCTAATGCTTCCCTGGGCAACCGCCCACCTACCACCCCCACCCCAG
Seq C2 exon
GCGGAGGAAGCAATGGCCACCTACCGTACATGCGTGGCCGATGCTAAGACACAGAAGCAGGAGCTGGAGGATACCAAGGTGACGGCACTACGGCAGATCCAGGAGGTCATCCGGCAGAGTGACCAGACCATCAAGTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020772:ENSBTAT00000027682:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.958 A=NA C2=0.804
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:
TGCAGCCTCCAAGACCCTG
R:
CGACTTGATGGTCTGGTCACT
Band lengths:
196-420
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]