DreINT0095849 @ danRer10
Intron Retention
Gene
ENSDARG00000079105 | mhc2dab
Description
major histocompatibility complex class II DAB gene [Source:ZFIN;Acc:ZDB-GENE-980526-200]
Coordinates
chr8:36435168-36435732:-
Coord C1 exon
chr8:36435451-36435732
Coord A exon
chr8:36435282-36435450
Coord C2 exon
chr8:36435168-36435281
Length
169 bp
Sequences
Splice sites
5' ss Seq
GGAGTAAGA
5' ss Score
4.36
3' ss Seq
ATTATTTCCTTTTACCACAGATC
3' ss Score
8.79
Exon sequences
Seq C1 exon
TACTACCAGAGGTAACAATCAAGTCAGTGAGGCAGGCTGAAGGCAGACATCCAGCTGTGTTGCTGTGCAGTGCATATGAATTCTACCCTAAAAAAATCAAAATGTCCTGGCTGAGAGATGGTAAAGAGGTGACCTCAGATGTGACCTCCACTATGGAGATGGCTGATGGAGACTGGTACTATCAGATTCATTCTCACCTGGAATACACCCCTAAATCTGGAGAGAAGATCCAATGTTTGGTGGAGCACGCCAGCTTAACTCAACCTCTTACTAAAGATTGGA
Seq A exon
GTAAGAGGGAACATTACTTCATTTCCATTTTGTCTTTCCTTCTTGACTTTTTTGTTTAAATAGAAAACACAGTACATATTTTGTTGTCACACTTGCATGGCTAAAACACTTTTAAATGTAAATAAAATTGTTGAATTTACTAACAGATTATTATTTCCTTTTACCACAG
Seq C2 exon
ATCCCCATATCTCTGAGTCTGACAGGAATAAATTTGCCATCGGAGCATCTGGTCTGGTGCTGGGAATCATCATAGCGATTGCTGGACTCATTTACTACAAGAAGAAATCAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000079105:ENSDART00000111240:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.011 A=NA C2=0.026
Domain overlap (PFAM):
C1:
PF122723=DUF3610=PD(23.5=24.2),PF0765410=C1-set=WD(100=87.4)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATGTCCTGGCTGAGAGATGGT
R:
ATTCCCAGCACCAGACCAGAT
Band lengths:
248-417
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]