MmuINT0075636 @ mm10
Intron Retention
Gene
ENSMUSG00000091705 | H2-Q2
Description
histocompatibility 2, Q region locus 2 [Source:MGI Symbol;Acc:MGI:95931]
Coordinates
chr17:35343113-35345030:+
Coord C1 exon
chr17:35343113-35343388
Coord A exon
chr17:35343389-35344754
Coord C2 exon
chr17:35344755-35345030
Length
1366 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCAG
5' ss Score
4.95
3' ss Seq
TTCTTAAATCTTCCACACAGATC
3' ss Score
8.54
Exon sequences
Seq C1 exon
GCTCTCACACTCTCCAGTGGTTGGTTGGCTGTGACCTGGGGCCAGACGGAAGCCTACTCCGAGGGTATGAGCAGTCTGCCTACGATGGCCGCGATTACCTCGCCCTGAATGAGGATCTGATAACGTGGACAGCGGCGGACCTGGCAGCACTGAAGACCCGAAGCAAGTTGGAGCAGGCTGGTCTTGCAGAGAAGCGCAGGGCCTACCTGGAGGTCGATTGCTTGACGTGGCTCCGCAGATACCTGGAGCTCGGGAAGGAGACGCTGCTGCACACAG
Seq A exon
GTGCAGGGGCCCTCGGGCAGCTCCTCCCTCTGCCCTCGGGCTGGGGCTCAGTCCTGGGGAAGAAGAAACCCTCAGCTGGGGTGATGCCCCTGTCTCAGAGGGGAGAGAGTGACCCTGGGTCTCCTGATCCCTCATCACAGTGACTGCACTGACTCTCCCAGGGCTCAGCCTTCTCCCTGGACAGTGCCCAGGCTGTCTCAGGAGGGAAGGAGAGAATTTCCCTGAGGTAACAACAGCTGCTCCCTTCAGTTCCCCTGTAGCCTTTGTCAGCCATGGCCTCTCCCAGGCCGGGTTCTCTGCCCACACCTACTGTGTGTGGACACTGACTCCTGTCCTGCTGAGTGTGTCAGCCCTTGCACCTCAGGACCTGAAGTCGCCTTTACCTGATGGGAGATATGGACTCCCCTACACTAGGCTAATTTGCCCAGTATCTAGAATTTTCATAGAGTACATTTTCATAGATCCCTCCCAGTCTGTTGGGTTTGCATCCCTTCCACAACCCAATTCTCTCTATTCCTACAGTGGTGAATGGTCATGTGAGCCCTTATGGGTACCCTGGAGGAATATAAATCGAGAAATTTCTTTTACTTATTTATCTGTTTTCTTATTCTTCTTTCTTTTCTCTTTACTTTTTCTTTATTTTTGAAGGTGTTATTTTGTTTCTAGTCAGTTTTTGTCTGCACTGGAGTGATCCTGTTTCTCCCTGCCCTTGTATTATCATTTGTATCAGTCTCCACAGGTGCCAGGGGAGACTGCTAACTTGGATAATTAGACGGGTTAAAACAAGGTTCTCATTAAATAACAGATTCTTGTGAACTTAGAGTGTTTCCTGTCAGAACTAAACATCCAGAAGCCTCCTGCTCTCCCTCTGCCCCACAAGTTACAGTGCCCCCCCCCCCAGTGAATCAGGACTTGGACTCTGAGAGACAGGGTCTTCTGCAATCCAGGGCTGAGTGAGAGGGAAGACCACACACCCTGTGAGCCCACTGTGTTCCAGTGAGGTCCACAGATCACTTCAAGTGTCCTGCTTAAAACACCTGTACCTTGTCCCCCAGAGTCAGGGGCTGGGAGTCATTTTCTCACTACACACTTTGTGATGGCTGTTCTCTTGGACTGACAGTTAATGTTGGTCAGCAAGATGACCACAGTGGTTGAGTCTCAGTGGATTCCCTCTTTGCTTCTAAGTCCCAAAAGAAAATGTGTAGTTCTGTGCTGAGGGGACCAGCTCTGCTTTTGGTCACTGTGCAACGACAGTTGTAGTGTCAAACAGACAAATAATTCACTGTCATCATTGATTTAACTGAGTCTTGAGTAGATTTTAGTTTGTCTTGTTAAAATCCTGTGATTTCTTAAATCTTCCACACAG
Seq C2 exon
ATCCCCCAAAGGCGCATGTGACCCATCACCCCAGTTCTCAAGGTGATGTCACCCTGAGGTGCTGGGCCCTGGGCTTCTACCCTGCTGACATCACCCTGACCTGGCAGTTGAATGGGGAGGACCTGACCCAGGACATGGAGCTTGTGGAGACCAGGCCTTCAGGGGATGGAACCTTCCAGAAGTGGGCATCTGTGATGGTGCCTTTTGGGGAGGAGCCTAGATACACATGCCATGTGGAACATGAGGGGCTGCCTGAGCCCCTCACCCTGAGATGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000091705:ENSMUST00000074806:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.011 A=NA C2=0.272
Domain overlap (PFAM):
C1:
PF0012913=MHC_I=PD(49.2=94.6)
A:
NA
C2:
PF0765410=C1-set=WD(100=89.2)
Main Inclusion Isoform:
NA
Other Inclusion 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:
TGAAGACCCGAAGCAAGTTGG
R:
TCTAGGCTCCTCCCCAAAAGG
Band lengths:
347-1713
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