DreINT0078468 @ danRer10
Intron Retention
Gene
ENSDARG00000062049 | hmha1b
Description
histocompatibility (minor) HA-1 b [Source:ZFIN;Acc:ZDB-GENE-071213-2]
Coordinates
chr22:17601480-17601822:-
Coord C1 exon
chr22:17601742-17601822
Coord A exon
chr22:17601648-17601741
Coord C2 exon
chr22:17601480-17601647
Length
94 bp
Sequences
Splice sites
5' ss Seq
CTGGTAACA
5' ss Score
4.6
3' ss Seq
TGATGTGTGTTTGAGCGCAGATG
3' ss Score
4.05
Exon sequences
Seq C1 exon
CCTCTGATGGTCCGCAAACAAGAGCATGAGAAGAAACGCAAAGAGATCAAGGAGCAGTGGCTGAAGGCCAAAAGAAAACTG
Seq A exon
GTAACATTTACATTTGTGCATCATCTGAGCTCACTGAACACCGTTTATAAACACAGATGCAGATCTGTAAGAGGTGATGTGTGTTTGAGCGCAG
Seq C2 exon
ATGGAGTGTGACGTGAACCTACGCAGGGCTAAACAGGTCTACATGACCCGCTGTGAAGAATATGATAAAGCCAGGACAGCGGCGAACAGGGCCGAGGAGGAGGGCGGCAGTGCCACCACCAAAACACTGGACAAGAAGAAACGACTGGAGGAAGAGGCCAGAAACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000062049:ENSDART00000132565:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.185 A=NA C2=0.589
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAGAGATCAAGGAGCAGTGGC
R:
TGTCCAGTGTTTTGGTGGTGG
Band lengths:
174-268
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]