BtaINT0072793 @ bosTau6
Intron Retention
Gene
ENSBTAG00000020772 | HMHA1
Description
histocompatibility (minor) HA-1 [Source:HGNC Symbol;Acc:HGNC:17102]
Coordinates
chr7:45191076-45191839:+
Coord C1 exon
chr7:45191076-45191184
Coord A exon
chr7:45191185-45191560
Coord C2 exon
chr7:45191561-45191839
Length
376 bp
Sequences
Splice sites
5' ss Seq
TTGGTGAGT
5' ss Score
9.27
3' ss Seq
CTCTCCCTTGGACTTTTCAGAAC
3' ss Score
7.77
Exon sequences
Seq C1 exon
GATGGGGTATCCAGCCAGCGACCCGAGGTGGTGGTCCAGGCACCGTACCTGGGGGGCAGCGGGGGTGCAGCCTTTCCCTTGACAGAGGAGGCTGAGGATGGGGTCCTTG
Seq A exon
GTGAGTTGGGTGGCCCTGGAGGTGCTGGGCAGATGGGGGGTGATGTAGTGGGTCCATGTCAAGGGCTGCAGACTGAACTGTTTCCCCAGACACAAGTGTTACCTGTCTTTAATCTGTTACAAACCCTTGCAAAGAGATACCCTTTCAAGGTGTTTTGCCAGGTCCAAGAAACAGGCACGCAGAAGTGGAAACAACCCCATGTATCTGAGACCCTGCACCTGATTTGAGAGGGTTCTGAGCAGGGAGACAGGCCTGCTGGGGGGGTGGGGGAGCCTCTTGGTGTCACCAGAGGCAGATGCCCAGTGGTTCCACCCCCAGCTCACAGGCCGTCCATCTGTCCCTCTGAATCTCTGTCCCTCTCCCTTGGACTTTTCAG
Seq C2 exon
AACCCCATGTCGCCTCCAATGACTCCGACTCAGAGCTGGAGGAGGCCTCAGACCTGCAGTCCCCGGTGGGTGGGGCTGCACTGCACCGGCTCAGTTTTCTGGAGAGGCAGGGCGGCGAGGCAGGCACAGAGGGCAGTCAGGGCAGCCGCAGCGGCAGCGAAGAGCAGCTGGGTGCCACAGCCGGCGAGTACGGGCCTGGGGCCTGGGAGGGCCCTGGGGAGGAGCCAGCCCGGAGGCTCTCCGAGTACAACACCAACCAGTGCAACAACACCAGCCAGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020772:ENSBTAT00000027682:22
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.838 A=NA C2=0.926
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
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTCCAGGCACCGTACCT
R:
TGTTGCACTGGTTGGTGTTGT
Band lengths:
344-720
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]