GgaINT0123603 @ galGal4
Intron Retention
Gene
ENSGALG00000000166 | DMB2
Description
Major histocompatibility complex class II beta chain BMA2, (similar to HLA class II, D beta chain) precursor [Source:RefSeq peptide;Acc:NP_001128638]
Coordinates
chr16:77016-78554:-
Coord C1 exon
chr16:78224-78554
Coord A exon
chr16:77301-78223
Coord C2 exon
chr16:77016-77300
Length
923 bp
Sequences
Splice sites
5' ss Seq
GGAGTGAGC
5' ss Score
2.46
3' ss Seq
CATCCCTGTCCCCACTCCAGCTC
3' ss Score
7.87
Exon sequences
Seq C1 exon
ATGAGGTCGCTGCCAGCACTGCCATCTCCCCTCTATCCCCCCAATGCAGGTGCCTTCATGGTGCATGTGGCCAACTCCTGCCCACTGGCAGCCAATGGCTCTCTGCGCGGCTTCGACCTCACCGTGGCCTTCAACAAGAACCCTCTGGTGTGCTACGACCCCGATGGCCACCTCTTCAACGCCTGCGACTGGGGGCTGCTGCACGGCGTGGCTGGACAGATTGCCATTGCCCTCAACAATGACAGCACCTGGGTGCAGCGTGCAGAGGCACGGAGACGGGCGTGCAGCAAACTGGCTGCACAGTTCTGGGCACAGACGGCGCTGCGCAGGA
Seq A exon
GTGAGCATTGCAAATGGGGCTGTTGCACGGGGCGTTGCATGGGGATGATGTTGCATGGGGCATTGCATGAAGATGGTGCTGCATAGGGCGTCGCATGGGGATGTTGCATGAAGATGTGTAGCAATGATGCATGGGACATTCCATGGGGATGCTGCATGAGGGTGTTGTTTAGCAATGATGCATGGGGTGCTGCATGGGAATGTTGCATGAAGATGTGTAGCAATGATGCATGGGGCATTCCATGGGGAGGCTGCATGAGAGCGCTGTGTAGCAATGATGCATGGGGTGCTGCATGGGGATGTTGCATGGAGATATTGCATGGGGCATTGCATGGGGTTGATCCATGCAGCGTTACATGGGGTTCTCAAGCAGGGGGATGTTGCATGGAAAGGTTGCATGGAAAATTGCACAGAGGTGTTGCAAAGCATATGCATGGGGATGTTGTATGGAGGATCGGACGGTGGCTTTGAAGAACATTCTGCATGGGGCATTGCTTAAGGGTCCCAAGCATGGGGATGCTGCAAGGAAATGCTGCTGCTTGGTGGCCTTGCAGAGTGTGTTGCATGGAGTTTGCTTCAAGGAGATGTTGCATGGCGTATCATCTGCAGTTTTGCAGAGCACATTGCATTGCACATTGCACACTGCACAGAGCAGTGCACTGGGCATCTCCCAGCGTGTGGCACAACGCTGTTGCAAAGGACATCCCACGAGGTGTTGCAGCAAACAATGCGCAGAGCTTGCACAGAATGTGGGATATCCCATGGAGATGTGGCACAGAGCATTGCGTGGGGAATCCTACAGGGAAGTGAGATGGGGAAGTTGCACAGAGCGTTGCAAGGGGTATTGCACAGAGGGAACTTGCAGAGAATGGGGCAGGAACCGTCCCCATCCCCTGCTGCTCACCATCCCTGTCCCCACTCCAG
Seq C2 exon
CTCAGCCCCAGGTCCGCATCGTCCCCGCACAGACAGGGAACCCCAGCGTGCCCATCCGCCTCACCTGCCACGTGTGGGGCTTCTACCCCCCCGAGGTGACCATCATCTGGCTACACAATGGGGACATCGTGGGGCCTGGAGACCACTCGCCCATGTTCGCCATCCCCAATGGGAACTGGACCTACCAGACACAGGTGGCCCTCTCGGTGGCCCCAGAGGTGGGGGACACCTACACGTGCTCGGTGCAGCATGCTAGCTTGGAGGAGCCCCTCCTGGAGGACTGGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000000166:ENSGALT00000000222:1
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=0.047
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0765410=C1-set=WD(100=87.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Human
(hg19)
No conservation detected
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCACCGTGGCCTTCAACAAG
R:
CGATGTCCCCATTGTGTAGCC
Band lengths:
343-1266
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]