BtaINT0072787 @ bosTau6
Intron Retention
Gene
ENSBTAG00000020772 | HMHA1
Description
histocompatibility (minor) HA-1 [Source:HGNC Symbol;Acc:HGNC:17102]
Coordinates
chr7:45188794-45189433:+
Coord C1 exon
chr7:45188794-45188966
Coord A exon
chr7:45188967-45189244
Coord C2 exon
chr7:45189245-45189433
Length
278 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGT
5' ss Score
10.03
3' ss Seq
CTCACACTGCCCACCCCCAGTGC
3' ss Score
6.94
Exon sequences
Seq C1 exon
CTGACCTCAATGGCATGACTCCAGAGCTGCCTGTGGCTGTGCCCAGCGGGCCCTTCCGCCACGTGGGGCTGTCCAAGGCGGCCCGGACCCACCGGCTTCGGAAGCTCCGCACACCGGCCAAGTGCCGGGAATGCAACAGCTACGTGTACTTCCAGGGCGCCGAGTGTGAGGAG
Seq A exon
GTGAGTGGTTCCGGTCGGGTCCAGGGGAGCCAGGCACCTGGATGTGCGTCCCATGTCGGGAGAGAGCACCTGCGGTCTGGAGGTGGGGCCAGAGCAGTGGGAGGAGCCCAGGCTGAAGGGTGAAAACTATTTCAGAAGCTGCACTGTGGTGGGGAGTCAGGGGTGGGGTGGGGGTGTGTGTTTGTGTGCGCGTGCACTGAGATGAGGCAGGAGATGGAGCCAGGGATGTCTGAGCTGGACCAGAGTCAGGTAGGGCTGCTCACACTGCCCACCCCCAG
Seq C2 exon
TGCTGCCTGGCCTGCCACAAGAAGTGCCTGGAGACCCTGGCCATCCAGTGTGGCCACAAGAAGCTGCAGGGCCGTCTGCAGCTCTTTGGCCAGGACTTCAGCCGTGCTGCCTGCAGCACCCCCGACGGCGTGCCCTTCATCATCAAGAAGTGCATCTTTGAGATCGAGCAGCGGGCGCTGCGCACCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020772:ENSBTAT00000027682:17
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.241 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0013017=C1_1=PU(57.1=48.3)
A:
NA
C2:
PF0013017=C1_1=PD(38.8=30.2),PF0062022=RhoGAP=PU(10.4=28.6)
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:
ATGACTCCAGAGCTGCCTGT
R:
TCTTGATGATGAAGGGCACGC
Band lengths:
307-585
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]