DreINT0078471 @ danRer10
Intron Retention
Gene
ENSDARG00000062049 | hmha1b
Description
histocompatibility (minor) HA-1 b [Source:ZFIN;Acc:ZDB-GENE-071213-2]
Coordinates
chr22:17597390-17597776:-
Coord C1 exon
chr22:17597586-17597776
Coord A exon
chr22:17597512-17597585
Coord C2 exon
chr22:17597390-17597511
Length
74 bp
Sequences
Splice sites
5' ss Seq
CCAGTAAGA
5' ss Score
5.9
3' ss Seq
TAATGTGGTGTTTATTTCAGGCA
3' ss Score
7.98
Exon sequences
Seq C1 exon
GCCACCATCTCCTACTACCAGATCATGCACATGCAGACGGTCGCGCTGCCGGTCCACTACCAGACTCTGTGCGAGAGCAGTAAACAGTACGACCCGGGACAGCAGTACGGCACGCACGTCAAAGACCTTCAGATGAGCGAAGAACCTGAAACGCATTATGAGTTTGAGGCCTACTCTGCCTCCTCTGTCCA
Seq A exon
GTAAGACACGCATACTAAAACATGTATTCTGAAAGTTGCTGTGAATGTTACTTTTAATGTGGTGTTTATTTCAG
Seq C2 exon
GCAGTCGGTTAGGCCGCGCACCGACAGCGCTAATGCTGAAGCTCAGAGCAGTGCTGAGGTGCCACAAACTGCAGGAGAGACTGGAGACACGAGCAGCTCACAGAAAGATGATCAGAAGAGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000062049:ENSDART00000132565:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.656 A=NA C2=1.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGCACGTCAAAGACCTTCAGA
R:
GTCTCCAGTCTCTCCTGCAGT
Band lengths:
167-241
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]