MmuINT0075531 @ mm9
Intron Retention
Gene
ENSMUSG00000067341 | H2-Eb2
Description
histocompatibility 2, class II antigen E beta2 [Source:MGI Symbol;Acc:MGI:95902]
Coordinates
chr17:34470228-34471435:+
Coord C1 exon
chr17:34470228-34470494
Coord A exon
chr17:34470495-34471153
Coord C2 exon
chr17:34471154-34471435
Length
659 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGC
5' ss Score
10.22
3' ss Seq
CACCTCCTTTTCTCCTCTAGCTG
3' ss Score
10.64
Exon sequences
Seq C1 exon
CACGTTTTCTGGAGCAGTTGAAGGCTGAGTGTCACTACTTCAATGGGAAGGAGCGTGTGTGGAGTGTGACCAGATTCATCTATAACCAGGAAGAGTTTGCCCGCTTTAACAGTGACTTTGGGAAGTTCCTGGCAGTGACTGAGCTGGGGCGGCCCATAGTTGAGTACTTGAACACCCAGAAGGACATGCTGGACAATTATCGTGCCTCAGTAGACAGGTGCAGAAATAACTATGACCTTGTGGATATCTTCATGTTGAACTTAAAAG
Seq A exon
GTAAGCATTAGATAGAGAGTAGATGGGTTGAGGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTAAAAGAGACAGTCAGCAGACAGACAGACAGACAGAGAAGAGAGAGGAGAGTTCTGTGTCACGTGTGTGGAGATCATAAGACAGGTTACCAGTCTCATTCTCGCCATCCATCCTATGGTCCTGAGAAATGAATTCAGACCGTCAGTCTTGGAAGCAAGCACCTTTATCTACTGAACCATCACCTAGCTCTTACCGTAATGACTTTTTAACTTTTTCTTGCATTGGGACGCCTGAGAACCAACTCTTTCTGTTTCCTGCTTCCCAGGGTAGAACCATTCCTGAGCTGTTCTCTGATATATGTGCTTTGAAGTTCTGTATTCATGATCTCTACATACTCTACTTTCAGGCATATTTTCAAACTGAAAATATTTCAGTTCAATAAAGAATTACTATTCCATGTTATAAAATAAGTCCTTATACTTTTTTTTCAGACCCAACAGATCCTGCTGTCAGGATTAACTTGAGGGACAGGTTTAGAATCCCTGAGATCTTCAGCCTGGGTGGATGGAGGCAGGTAGGCAGCCTACAGGGAGGACAGCTTTATCCTCAGGGTTCTTTCTCACCTCCTTTTCTCCTCTAG
Seq C2 exon
CTGAGCCCAAGGTGACTGTGTACCCTGCAAAGACACAGCCTCTGGAACACCATAACCTCCTGGTCTGCTCTGTGATTGACTTCTACCCTGGCAGCATTGAAGTCAGATGGTTCCGGAATGGCGAGGAGGAGAAGACTGGAGTTGTGTCCACTGGACTGATCCAAAATAGAGACTGGACCTACCAGACCCTGGTGATGCTGGAGATGGTTCCTCGGGGTGGAGAGGTTTACACCTGCCAGGTGGAGCATCCCAGCCTGACCAGCCCTGTCACAGTGGAGTGGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000067341-H2-Eb2:NM_001033978:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0096914=MHC_II_beta=WD(100=82.2)
A:
NA
C2:
PF0765410=C1-set=WD(100=87.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGGAGCAGTTGAAGGCTGAG
R:
ATGCTGCCAGGGTAGAAGTCA
Band lengths:
356-1015
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: