BtaINT0072791 @ bosTau6
Intron Retention
Gene
ENSBTAG00000020772 | HMHA1
Description
histocompatibility (minor) HA-1 [Source:HGNC Symbol;Acc:HGNC:17102]
Coordinates
chr7:45189897-45190417:+
Coord C1 exon
chr7:45189897-45190123
Coord A exon
chr7:45190124-45190206
Coord C2 exon
chr7:45190207-45190417
Length
83 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
TGCACCCTACAACCCCCCAGGAT
3' ss Score
5.11
Exon sequences
Seq C1 exon
CTCCCTGAGCCGCTCATTTCCTTCCGCTTCTACCATGAGCTTGTGGGGATGGCCAAAGACAGTCTGAAGGCCGAGGCCGAGGCCAAGGCAGCATCTCGGGGTCGGCCGGATGCCACAGAGAGGGAGGCTGCAGCCATGGCCATGGCGAGCCGGTTGCGGGAACTCCTACGGGACCTGCCTCGGGATAACTGGGCCACACTGCGGTACCTGATGCGGCACCTGCGCAG
Seq A exon
GTGAGGGCCGAGTCGGCCAGGGTCAAGGGTGGCAGGGTCCTGGGAGCTGCTCACACCTGCCCCTGCACCCTACAACCCCCCAG
Seq C2 exon
GATCGTGGAGGTGGAACAGGACAACAAGATGACACCAGGGAACCTGGGCATTGTGTTTGGGCCCACGCTGCTGCGGCCCCGGCCCACTGAGGCCACGGTGTCCCTTTCCTCCCTGGTGGACTACCCCCACCAGGCCTGCATCGTGGAGACCCTCATCACCCACTTCAGCCTGGTCTTCAAGGAGGAGCCCGAAGAGGCCCCAGGGGGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020772:ENSBTAT00000027682:20
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.250 A=NA C2=0.239
Domain overlap (PFAM):
C1:
PF0062022=RhoGAP=FE(43.4=100)
A:
NA
C2:
PF0062022=RhoGAP=PD(18.5=45.1)
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:
GGATGCCACAGAGAGGGAGG
R:
AAACACAATGCCCAGGTTCCC
Band lengths:
178-261
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]