MmuINT0075623 @ mm10
Intron Retention
Gene
ENSMUSG00000079507 | H2-Q1
Description
histocompatibility 2, Q region locus 1 [Source:MGI Symbol;Acc:MGI:95928]
Coordinates
chr17:35321275-35323339:+
Coord C1 exon
chr17:35321275-35321550
Coord A exon
chr17:35321551-35323063
Coord C2 exon
chr17:35323064-35323339
Length
1513 bp
Sequences
Splice sites
5' ss Seq
CAGGTCTCT
5' ss Score
1.07
3' ss Seq
TTCTTAAATCTTTCACACAGACC
3' ss Score
7.75
Exon sequences
Seq C1 exon
GCATTCACACCTTCCAGAAGTTGTCTGGCTGTGATCTGGGGTCAGATGGGCGCCTTCAAAGCGGGTACCTGCAGTTCGCCTATGATGGCCTTGATTACATCGCCCTGAATGAAGACCTGGAAACCTGGACAGCAGCAGATGTGGCAGCTCAGGAAACCCGACGCAAGTGGGAGCAGGCTGGTGCTGCTGAGAAACACAGGACCTACCTGGAGGGCAAGTGCCTGATGTGGCTCCACAGATACCTGGAGCTCGGGAAGGAGATGCTGCTGCGCACAG
Seq A exon
GTCTCTGGCTGGGGCTCAGTCCTGGGGAAGAAGAAACCCTCAGCTGGGGTGATGCCCCTGTCTCAGAGGGGAGACAGTGTCCCTGGGTCTCCTGATCCCTCATCACAGTGACTGCACTGACTCTCCCAGGGCTCAGGCTTCTCCCTGGACAGTGCCCAGGCTGTCTCAGGAGGGAAGGAGAGAATTTCCCTGAGGTAACAACAGCTGCTCCCTTCAGTTCCCCTGTAGCCTCTGTCAGCCATGGCCTCTCCCAGGCTGGGTTCTCTGCCCACACCCACTGTGTGTGGACACTGACTCCTGTCCTGCTGAGTGTGTCAGTCCTTACACCTCAGGACCGGAAGTCTCCTTTCCCTGACATGGACTCCCCTACACTAGGCTGGTTGCCCCAGTTTCTAGAATTTTCTAAAGAATACATTCTCCCAGATCCCTCCCTGTCTGTGGGGTTTGCACCCCTTCGACAACCCAATTCTCTTTATTCCTACACTGGTGAATGGTCACATGAGGCCTTATTGGGAACCCTGGAGGAATATAAATCATGGAATTTCTTTTTCTTTTTTTCTCTCTTTTCTTTTTCTTCTTTCTTTCTTTTTTCCTTACTTTTTTTTTTTTGTGGAAGGCATTATTTTGCTTGTAGTCATCTTTTGTCTGCACTGGAATGATCCTGTTTCTCCCTGCCCTTGTATTATCATGTGTATCAGTCTACACAGGTGCCAGGGAAGGCTGCTAACCTGGATAATTTGACAAGTTAAATCAGGGTTCTCATTAAAGGAGAGATTCCTGTGAACTTAGAGTGTTTCCTGTCAGAACTAAACACCCAGAAGCCTCCTGCTCTTCCTCTGCCCCCCACAAGTTACAGTGCCCCCCCCCCCCAGTGAATCAGGACTTGGACTCTGAGAGACAGGGTCTACTGCAATCCAGGGCTGGAGTGAGAGGGAAGACCACACACCCCGTGAGCCCACTGTGTTCCAGTGAGTGCTGCACTGGGGTCCACAGCTCACTCCAGGGATCCTGTGTGACACACCTGTACCTTGTCCCCCAGAGTCAGGGGCTGGGAGTCATTTTCTCTGGCTCATCACTTAGTGATGGCTGTTCACTTGAACTGACAGTTAATGTTGGTCGACGAGATGACAACAGTTGTAGTCTCAGTTTTAGCACCCTTTCAGTAGCATATGTGCCTAATATCTGATTTTGATATGAACTCAAACACATAATAAATTACTTATTTTCCATTCCCTCTTCCATTCTTTGACTACGTCTCTCATGCTATCTAACATTACATAAGGATGACCATGGTGATCCACTGGCTCATGTGGATTCCATCATAGCTTCTGAGTCCCAAAAGAAAATGTGCAGTTGTGTGCTCAGGGACCAGCTCTGCCTACTGGTCACTAGTGTGATGACAGTTGAAGTGTCAAACGGACACGTAGTTCAGTGTCATCATTGTTTTACCTGAGTCTTGTGTAGATTTCAATTTGTCTTGTTAACCCTGTGATTTCTTAAATCTTTCACACAG
Seq C2 exon
ACCCCCCAAAGGCACATGTGACTCATCACCCCAGATCTCAAGGTGATGTCACCCTGAGGTGCTGGGCCCTGGGCTTCTACCCTGCTGACATCACCCTGACCTGGCAGTTGAATGGGGAGGAGCTGACCCAGGACATGGAGCTTGTGGAGACCAGGCCTGCAGGGGATGGAACCTTCCAGAAGTGGGCATCTGTGGTGGTGCCTCTTGGGAAGGAGCAGAATTACACATGCCATGTGTACCATGAGGGGCTGCCTGAGCCCCTCACCCTGAGATGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000079507:ENSMUST00000073208:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.065 A=NA C2=0.140
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
Chicken
(galGal4)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAACCTGGACAGCAGCAGATG
R:
AGATGCCCACTTCTGGAAGGT
Band lengths:
347-1860
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