MmuINT0075494 @ mm10
Intron Retention
Gene
ENSMUSG00000073421 | H2-Ab1
Description
histocompatibility 2, class II antigen A, beta 1 [Source:MGI Symbol;Acc:MGI:103070]
Coordinates
chr17:34267336-34268033:+
Coord C1 exon
chr17:34267336-34267617
Coord A exon
chr17:34267618-34267922
Coord C2 exon
chr17:34267923-34268033
Length
305 bp
Sequences
Splice sites
5' ss Seq
GGAGTAAGG
5' ss Score
4.33
3' ss Seq
CACTCAGCTCTATTCCCCAGGGG
3' ss Score
6.34
Exon sequences
Seq C1 exon
AACAGCCCAATGTCGTCATCTCCCTGTCCAGGACAGAGGCCCTCAACCACCACAACACTCTGGTCTGCTCAGTGACAGATTTCTACCCAGCCAAGATCAAAGTGCGCTGGTTCCGGAATGGCCAGGAGGAGACGGTGGGGGTCTCATCCACACAGCTTATTAGGAATGGGGACTGGACCTTCCAGGTCCTGGTCATGCTGGAGATGACCCCTCGGCGGGGAGAGGTCTACACCTGTCACGTGGAGCATCCCAGCCTGAAGAGCCCCATCACTGTGGAGTGGA
Seq A exon
GTAAGGGAATTTCTTTTTATTTCACTGTGGGCCCCACATGACATGGGATTTTAGGTGTTATTATCCCATCCCTCCAATGTCACCCACCCCATCACTTGTCCTATATGATCTGCTTCCACTACTGAGCTGAGACCTACAGGAAATCATATCTCTCACCTCATAGTCAGGGCATCAGGAGAGCCCTGACCTATCTTCTCAGACAGCAGTTCTGGAGATCACTATATACACTGGGGCCCTGGAACTTGTCCCTTATATCCAGAGGAATTGGCTGAAGTAGACTGTAGACACTCAGCTCTATTCCCCAG
Seq C2 exon
GGGCACAGTCTGAGTCTGCCTGGAGCAAGATGTTGAGCGGCATCGGGGGCTGCGTGCTTGGGGTGATCTTCCTCGGGCTTGGCCTTTTCATCCGTCACAGGAGTCAGAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000073421:ENSMUST00000040828:3
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=0.026
Domain overlap (PFAM):
C1:
PF0765410=C1-set=WD(100=87.4)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCTCAACCACCACAACACTC
R:
CTGTGACGGATGAAAAGGCCA
Band lengths:
343-648
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types