DreINT0078462 @ danRer10
Intron Retention
Gene
ENSDARG00000062049 | hmha1b
Description
histocompatibility (minor) HA-1 b [Source:ZFIN;Acc:ZDB-GENE-071213-2]
Coordinates
chr22:17592721-17593194:-
Coord C1 exon
chr22:17593057-17593194
Coord A exon
chr22:17592960-17593056
Coord C2 exon
chr22:17592721-17592959
Length
97 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAAC
5' ss Score
5.56
3' ss Seq
TGTGTGTGTGTTTTCTTCAGCTT
3' ss Score
10.3
Exon sequences
Seq C1 exon
GGCATTTATCGAGTGAATGGAGTAAAGACGCGGGTGGAGAAACTCTGCCAGGCATTTGAGAACGGCAAAGAGCTGGTCGAACTATCACAGTCATCTCCACATGACATCAGTAATGTCCTGAAGCTTTACCTGCGACAG
Seq A exon
GTGAACAAAACATCCATGAAAAACATTGAAGACATCTAGCAAAAACATTCAAAGTCAAATCCACTTAACTCTGTTTGTGTGTGTGTGTTTTCTTCAG
Seq C2 exon
CTTCCGGAGCCCATCATGCCCTTCCGCCTCTACAACAGTCTCATGGGTCTGGCCAAGGAAAGTCTGGCTGTTGTGGGTCCAGAGGGAGCTGACAGTGGTAAAGGACCAGACCTGATGGACCTTGGACCTGAGACGGATCCTGAACTCTTGGTCCTCGTGGACAGACTTAAAAATCTCCTGAAAGAGCTGCCCAAACCAAACACCGCCACGCTCCGCTACCTAGCGCGTCATCTGAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000062049:ENSDART00000132565:13
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.138
Domain overlap (PFAM):
C1:
PF0062022=RhoGAP=FE(25.4=100)
A:
NA
C2:
PF0062022=RhoGAP=FE(44.6=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:
TCTGCCAGGCATTTGAGAACG
R:
AACAGCCAGACTTTCCTTGGC
Band lengths:
167-264
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]