MmuINT0075492 @ mm10
Intron Retention
Gene
ENSMUSG00000073421 | H2-Ab1
Description
histocompatibility 2, class II antigen A, beta 1 [Source:MGI Symbol;Acc:MGI:103070]
Coordinates
chr17:34263209-34265033:+
Coord C1 exon
chr17:34263209-34263405
Coord A exon
chr17:34263406-34264760
Coord C2 exon
chr17:34264761-34265033
Length
1355 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGT
5' ss Score
9.72
3' ss Seq
CTGACCGCGTCCGTCCGCAGGGC
3' ss Score
10.82
Exon sequences
Seq C1 exon
GACACTCTGGGATTTCAGATCACTCCAGGCTACAGAACTTTGCTTTCTGAAGGGGGCACAGCAGGTGTGAGTCCTGGTGACTGCCATTACCTGTGCCTTAGAGATGGCTCTGCAGATCCCCAGCCTCCTCCTCTCGGCTGCTGTGGTGGTGCTGATGGTGCTGAGCAGCCCAGGGACTGAGGGCGGAGACTCCGAAA
Seq A exon
GTAAGTGCCGGGGGCAGGGCTCTCCAGAGCCAGCACTCTGGGGGTCGTGTTCTGAGGGACCCTGGGGACTCTGGGATGTGGGAGGGGGTGGCAAAATCCTGATTTTACTATAGATTTCCTTTCTCTGAAGAGAGAGTGAGACTCCATTCTCACTTCTGTGTTCTAATATTGAGTTAGGATGGTGCCGCCGCCGGTGCGAGCCTGACATATAAACGGAGGAGGAGGAGGAGGCGGCAGAATTTAAATCGACCACCAAAGATAAGGGTTGTGCATGGGGAGACAGCAGGGCTTACAATACCAGTGCCCCCACCCACTCCCCCGTACAGGGCTTACAATACCAGTGCCCCCCACCCCCACCCCGTACATTGTCTGGAGGAAATGCCAGATTCTGAAGTGGGGAAACAGATCAGCGATGGTCTGTGGTCCCGATGTTTGCGGACAACTCCTCATGTGGAGTGGAGGTTTAAGAGAGCGAACTCTAGGCGTCTAACTCAGAGAGAAGCCAGTGACCAAGAAACCTAATTTTTTTGGTCAAATGGAATCCAGAACTCAAACACTGAGTTAGTAAATTGAATTTCCAAGAAAACACTAGGCCCAGAAGGGACATATGTGATACATACCCTGGGGTGAGCGGAGGTGTCCTAGTTCGTTCGGAGACCAGAGAGTAAATAAAGCCCCAGTCCCCTAAGCCATAGAGGTGTCTTCAGTCTCGCAGTTACCCTTAAGATGCCTGGAGTGACCGTGCAAGCAGGCAGTTCTCAGAGGTTGCCTGGATTCCCATTTGTTGGTTTTGTAGTCGGGGCTCTCCTGAGAACGAGTGCCCCCTAGGGGGTCAGGGCCTTTTGCACACAGGAGAGAGTCCCACAGGGTGGGGGTGGGGTAGCAGAAACTGGCAAATATTTTATTTATTTTTTGTATCCTAGTTTTATTAGTTCGCTGAGAATTTCGTACAGTTTTGGTCATATTTACTCCCTCTTCCAACTCTACCCAGGCCCATCCCCCCCCCTCTACCACCCAACTTTTGGTGTCCCTTAGTTTTATTATTATTTTTTTTTTCAAATGTACCAAGTACCGTTTGCGTTTCCTGAGGCGTATTCTTGTGAGGACGAGCCCGGTCGCCCCATCCCTCCCTTCCTCTTCCTTACCCCGGGTCGAACCGTCGCCCGGTGCTCCGCCGAAGCGGGGTCCTCACGGGCGGGGGCGGCGAAGAGACTGCCCGGCCCGAGGCCCCGAGGCCCGACGGTCCCCAGAGAGCGGTCGCCCCACGCGGGAAGCGCCGGCGCGGGGTGGGGCCGCGGGGAGCCGTGGTCTGCGTGGTCCCCGCTGTCCCCCGGGCTGACCGCGTCCGTCCGCAG
Seq C2 exon
GGCATTTCGTGTACCAGTTCATGGGCGAGTGCTACTTCACCAACGGGACGCAGCGCATACGATATGTGACCAGATACATCTACAACCGGGAGGAGTACGTGCGCTACGACAGCGACGTGGGCGAGCACCGCGCGGTGACCGAGCTGGGGCGGCCAGACGCCGAGTACTGGAACAGCCAGCCGGAGATCCTGGAGCGAACGCGGGCCGAGCTGGACACGGTGTGCAGACACAACTACGAGGGGCCGGAGACCCACACCTCCCTGCGGCGGCTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000073421:ENSMUST00000040828:1
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=0.087
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0096914=MHC_II_beta=WD(100=81.5)
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:
ACCTGTGCCTTAGAGATGGCT
R:
CCCTCGTAGTTGTGTCTGCAC
Band lengths:
350-1705
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