MmuINT0075598 @ mm9
Intron Retention
Gene
ENSMUSG00000016206 | H2-M3
Description
histocompatibility 2, M region locus 3 [Source:MGI Symbol;Acc:MGI:95915]
Coordinates
chr17:37407943-37409489:+
Coord C1 exon
chr17:37407943-37408218
Coord A exon
chr17:37408219-37409213
Coord C2 exon
chr17:37409214-37409489
Length
995 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGA
5' ss Score
9.46
3' ss Seq
TCCACCTTTCCCCCACCCAGATC
3' ss Score
8.88
Exon sequences
Seq C1 exon
GCTCTCACATCCTGCAGTGGATGGTTTCCTGTGAGGTAGGGCCAGACATGCGCCTTCTTGGAGCCCACTATCAGGCTGCGTATGATGGCTCAGATTACATCACCCTGAATGAAGACCTGAGCTCCTGGACTGCAGTGGACATGGTGTCTCAGATCACGAAGAGCCGTTTAGAGTCAGCTGGCACAGCAGAGTACTTCAGGGCCTATGTGGAGGGAGAGTGCCTGGAGCTGCTCCACAGATTCCTGCGGAATGGCAAGGAGATTCTTCAGCGAGCAG
Seq A exon
GTATGAGGAACAACTAGGAACCACTTTTAGTAAGCAAAGATAACCCCCTCAAACATACAAGTGAGGCTCTTGATGTCTGGGGAGGGAGGAAATACCAGATCCGCTGGAATACTGCACAAGGAGGAGGAAGAGTGGTACTGGCCTTCCTGATCCAACATCAGAGAGTGACTGTCCCCAGGGCTGACCCTACTTTCAGAACATTTGAATCTGTCCCAGAATGGAAGGAGAAAACACCCTGAGATACACAACCAACCACTTCCATTCAGTCTGCAGCTCATTGTGTACCATGGCCTCTTTCAGGTCTGGTTCTCTCAACACCCCTAATGTCTTTGGAAGTCACACTGCACTAATGCTGTGAGTCTCTGCTCAACCTAATCAGGACTAGAGATGGGAAATGTGAAGCTCCCTACTAGATTTTCTCTTAGGGCTTCTATTGCTACAAAGAAACACCATGGCCAAAAGCAAGTTGGGGAAGAAAGGGTTTATTTGGCTTACCCTTTCAGCACTGTTTGTCATTGAAGAAAGTCAGGACAGAAAGTCAAATAACTGATCTACATGACATGGAGGAGTGCTGCTTCCTGTCTTGCACCCCATGGCTTGCTCAGCCTGCTTTCTTATAGAACCCAGACCTCAAGCCCAGCGATGGAACCACCCACAATGAGTTGGGCCCCACAGCATCAATCACTAATTAAGAAAATGACCTCTAGTCTTGCCTACAATTTGATCTTATGCTGTCATTTTGTTAACGGAGATTCCCTCCTCTCATATAACTTTAGTTTGTGTCAAGTTGACATAAAACTATCCAGTGCACTAACCCTGATTTTAGAACATTCCAAGGAATGGATCATGATAGGTCCCTGGATCCAGACTCCCGTATGGTGCTTACATCCCTCCTGTGCCCTAATTCTGTCCATCCAGAGGATGCTCCTATGATCTCCAATGACTCTCCAAAAATAATGCAAAATACTTGAATTTTCCACCTTTCCCCCACCCAG
Seq C2 exon
ATCCCCCAAAGGCACATGTGGCCCATCACCCGAGACCCAAAGGTGATGTTACCTTGAGGTGCTGGGCTCTGGGCTTCTACCCTGCTGACATCACCCTGACCTGGCAGAAGGATGAAGAGGACCTGACCCAGGACATGGAGCTTGTGGAAACGAGGCCTTCAGGGGATGGAACCTTCCAGAAGTGGGCAGCTGTGGTGGTGCCTTCTGGAGAGGAGCAGAGATACACATGTTATGTGCACCATGAGGGGCTAACCGAGCCCCTTGCCCTGAAATGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000016206-H2-M3:NM_013819:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.011 A=NA C2=0.194
Domain overlap (PFAM):
C1:
PF0012913=MHC_I=PD(49.2=94.6)
A:
NA
C2:
PF0765410=C1-set=WD(100=90.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping 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:
GAAGACCTGAGCTCCTGGACT
R:
CTGCCCACTTCTGGAAGGTTC
Band lengths:
355-1350
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: