DreINT0078458 @ danRer10
Intron Retention
Gene
ENSDARG00000062049 | hmha1b
Description
histocompatibility (minor) HA-1 b [Source:ZFIN;Acc:ZDB-GENE-071213-2]
Coordinates
chr22:17606349-17606697:-
Coord C1 exon
chr22:17606562-17606697
Coord A exon
chr22:17606411-17606561
Coord C2 exon
chr22:17606349-17606410
Length
151 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAGA
5' ss Score
8.91
3' ss Seq
TGCTTTGTATGTCTATTCAGAGC
3' ss Score
8.52
Exon sequences
Seq C1 exon
GCGATGAGCGCTGAAGAGGTGGACATCATCCTGCAGCGCAGTGAAGGCGGTGTGGACTCCGCTCTGACGTACGCTAAAACCATCTCCAAATACTTGAAGGATCTCATCGGATACGTAGAGAGGAAGCTTGCGCTGG
Seq A exon
GTAAGATCACATGTGCTTTCATTCATTTAAAATGGGTTACAAGTGTTACGTTACTATTATTATTATTAAAGTATCTCGTTTCTATATAAACCAGTTTAAAGTGACTACAGCAGAGCTCCTTTTATAATTACTGCTTTGTATGTCTATTCAG
Seq C2 exon
AGCTGGAGTTCTCCAAGGGTTTACAGAGGATCTATCAGTCGTGTAAACAGACCATCACACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000062049:ENSDART00000132565:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0061118=FCH=PU(40.7=80.4)
A:
NA
C2:
PF0061118=FCH=FE(22.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGATGAGCGCTGAAGAGGTG
R:
TGTGTGATGGTCTGTTTACACGA
Band lengths:
196-347
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]