BtaINT0072800 @ bosTau6
Intron Retention
Gene
ENSBTAG00000020772 | HMHA1
Description
histocompatibility (minor) HA-1 [Source:HGNC Symbol;Acc:HGNC:17102]
Coordinates
chr7:45186380-45187023:+
Coord C1 exon
chr7:45186380-45186432
Coord A exon
chr7:45186433-45186855
Coord C2 exon
chr7:45186856-45187023
Length
423 bp
Sequences
Splice sites
5' ss Seq
CAGGTCTGA
5' ss Score
5.06
3' ss Seq
TCAGAGTCCCACCTGCCCAGGTT
3' ss Score
2.56
Exon sequences
Seq C1 exon
TCTGCCCTTGGCAGCCCGATCCCGAATGGAGTCACATCTCCTCGTCTACTCAG
Seq A exon
GTCTGAGTCCTGATCCTTGAGTTTGGGGAGCCGAGAACCCCAGCCAGGGCTCGCGGGACTCCGGGGGCGGAGCTTTCCTCGGCGGGGGCGGGGTCTTCGGACCGGCCAGAGCTGGTTTGGCTGATGAAAACCCGGTACCAAAGACCCTAGGCCGTCGTGCGCATTCACGATCCCTGCGCTCTGATGGTATACCATGTGTATCTGCGGGACGGTGCACCCCGCGCTGGACCAGAGGCCTGTGCGCTGCCAGGCAGGGCCCCGAGGTGAGGGGATGGGCGGGGTGTGGGGGTGCAGGCTCTGGTCAGGAGCACGTGGTGCTCTGGGCATTTGCCGGCCCACTGGGGACACAAGGCTGCCGGGCGCTTACCTTGGCCGGTGCAGAGCTGGGCATGTCTGGGCTTCGTCAGAGTCCCACCTGCCCAG
Seq C2 exon
GTTGGGGTGCTGCGGGGACCCAGGTGGCGGAGGCCCAGGAGACACGAGGGGCGGGGTGCCTGGGAGGAATGTCTGGGGAAGGGGCGTGGCCGGCCTCCCTGGATTCCTGAAGCTCCTTCCGGCCTCCCGAAGCTCCCCGCTGATTCAGGCGCAAGTCCTGAATCCGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020772:ENSBTAT00000027682:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.333 A=NA C2=0.964
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Mouse
(mm10)
No conservation detected
Rat
(rn6)
No conservation detected
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:
CCCTTGGCAGCCCGATCC
R:
GGATTCAGGACTTGCGCCTG
Band lengths:
214-637
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]