MmuINT0075625 @ mm10
Intron Retention
Gene
ENSMUSG00000079507 | H2-Q1
Description
histocompatibility 2, Q region locus 1 [Source:MGI Symbol;Acc:MGI:95928]
Coordinates
chr17:35323467-35323812:+
Coord C1 exon
chr17:35323467-35323601
Coord A exon
chr17:35323602-35323779
Coord C2 exon
chr17:35323780-35323812
Length
178 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGA
5' ss Score
9.45
3' ss Seq
CACAGCTTTTCTTCTCACAGGTG
3' ss Score
9.69
Exon sequences
Seq C1 exon
AGCCTCCTCCATACACTGTTTCCAACATGGTAATCATAGCTGTTCTGGTTGTCCTTGGAGCTGTGATAGTCATTGGAGCTGTGGTCATCATTGGAGTTATGGTGTCTTTTGTGATGAAGAGGAGGAGAAACAAAG
Seq A exon
GTAGGAAAGGCCAGGGTCTGAGTTTTCTCATAGCCTTCTTTAGAGTGTCCTCTGCTCATTAAATGGAAACACAGCCACACCCCTCATTGCTACTGTCTCTAACTGGGTCAGCTGTCAGTTCCGGGAACTTCCTAGAGTCAAGATCTTCCTTGAACTCTCACAGCTTTTCTTCTCACAG
Seq C2 exon
GTGGACAAGGAGAGGACTGTGCTCTGGCTCCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000079507:ENSMUST00000073208:5
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=0.583
Domain overlap (PFAM):
C1:
PF066236=MHC_I_C=PU(6.9=4.3)
A:
NA
C2:
PF066236=MHC_I_C=FE(37.9=100)
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:
AGCCTCCTCCATACACTGTTTC
R:
CCAGAGCACAGTCCTCTCCTT
Band lengths:
162-340
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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