MmuINT0075636 @ mm9
Intron Retention
Gene
ENSMUSG00000079507 | H2-Q2
Description
histocompatibility 2, Q region locus 1 [Source:MGI Symbol;Acc:MGI:95928]
Coordinates
chr17:35480058-35481975:+
Coord C1 exon
chr17:35480058-35480333
Coord A exon
chr17:35480334-35481699
Coord C2 exon
chr17:35481700-35481975
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
ENSMUSG00000079507-H2-Q2:NM_010392:3
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=NA
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NA
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Human
(hg38)
No conservation detected
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
No conservation detected
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
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: