BtaINT0072790 @ bosTau6
Intron Retention
Gene
ENSBTAG00000020772 | HMHA1
Description
histocompatibility (minor) HA-1 [Source:HGNC Symbol;Acc:HGNC:17102]
Coordinates
chr7:45184755-45185391:+
Coord C1 exon
chr7:45184755-45185085
Coord A exon
chr7:45185086-45185320
Coord C2 exon
chr7:45185321-45185391
Length
235 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGA
5' ss Score
7.23
3' ss Seq
TGTCATGTGCATAGAAATACAAA
3' ss Score
-11.22
Exon sequences
Seq C1 exon
GAGCTGCCTAGGAGAGACGGGGCTGATGCAGTGTCCCTGGGGCCCAGCCTAGAACCCCCAAGTGTGGCCTCGAATGCTAAGGCCACAGGCACTCTCAAGAGGCCAACCAGCCTGAGCCGCCATGCCAGCGCTGCTGGCTTCCCTCTGTCGGGGGCCAGCACTTGGACGCTGGGCCGCAGCCATCGCAGCCCACTGTCTGCGGCCAGCCCGGCCGAGGCACCCATCCAGGGACCCTGCCCAGACACCGTGGAGGACATCTCCCACCTGCTGGCTGACGTGGCCCGCTTTGCCGAGGGTCTTGAGAAACTGAAGGAGTGTGTTCTGCATGATG
Seq A exon
GTGAGAACTGGCAGGGACACCAAGGCCTGGGTGGAGGAAAGCAGGGTCAGACCTTAAAACCTAGGGGGTCAGCACAGAGTTGGGGAAGGACTTGGGGAGGCTCAGATGGAAATGGTTCGGAGGGCTTTGTGGAAAAAGACATTGCAGCTAGGGTTCTGACAGATGAATAGGAGTTCAGTGGCAACTAGGAAAGAAAGGCATTGAGGTAGAGGGAATGTCATGTGCATAGAAATAC
Seq C2 exon
AAAGTAGAGATGCATTGGGGGGAATAAGGTTCAGGTGTATGAAATGTGTAAGGCTGAAGACATTGAGAATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020772:ENSBTAT00000027682:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.523 A=NA C2=0.000
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
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCGAATGCTAAGGCCACAGG
R:
ACACCTGAACCTTATTCCCCC
Band lengths:
301-536
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]