BtaINT0072783 @ bosTau6
Intron Retention
Gene
ENSBTAG00000020772 | HMHA1
Description
histocompatibility (minor) HA-1 [Source:HGNC Symbol;Acc:HGNC:17102]
Coordinates
chr7:45187852-45188285:+
Coord C1 exon
chr7:45187852-45188042
Coord A exon
chr7:45188043-45188160
Coord C2 exon
chr7:45188161-45188285
Length
118 bp
Sequences
Splice sites
5' ss Seq
CTGGTACAC
5' ss Score
2.74
3' ss Seq
TTGGCTGTTGGTCCCACCAGGTC
3' ss Score
8
Exon sequences
Seq C1 exon
GCCACCATCTCATATTACCAGATGATGCACACGCAGACGGCCCCACTGCCCGTGCACTTCCACATGCTGTATGAGAGCAGCAAGCTGTACGACCCAGGCCAGCAGTACGCTTCCCATGTGCGCCAGCTGCAGCGCGGCGAGGAGCCTGATGTGCACTACGACTTCGAGCCCCACGTGTCCGCCAGTGCCTG
Seq A exon
GTACACTACCTTCTGCGCATGCCCAGGGAGCCAGACTTCCTGCCTGAGATGAGGGCAGGGGCAGGGAGCCCTTGTGACCCCCATCACAGCCCCTCCTTTTGGCTGTTGGTCCCACCAG
Seq C2 exon
GTCCCCAGTCCTGCGTGCTCGGAAAAGCAGCTTCAATGTCAGCGATGCTGTGGGGGCAGAGGCTGCCAGTAGCCCCCCGGAGGACGGCGGGCCCAGCCAGGGAGAGATTGCCAAGGAGCGCAGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020772:ENSBTAT00000027682:13
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.469 A=NA C2=0.651
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
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGCTGTATGAGAGCAGCAAGC
R:
TCCTTGGCAATCTCTCCCTGG
Band lengths:
244-362
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]