MmuINT0075508 @ mm10
Intron Retention
Gene
ENSMUSG00000073411 | H2-D1
Description
histocompatibility 2, D region locus 1 [Source:MGI Symbol;Acc:MGI:95896]
Coordinates
chr17:35266688-35267499:+
Coord C1 exon
chr17:35266688-35266726
Coord A exon
chr17:35266727-35266865
Coord C2 exon
chr17:35266866-35267499
Length
139 bp
Sequences
Splice sites
5' ss Seq
AAGGTGACA
5' ss Score
5.19
3' ss Seq
TCATGACTCTCATTCTCTAGCGT
3' ss Score
7.06
Exon sequences
Seq C1 exon
GCTCCCAGAGCTCTGAAATGTCTCTCCGAGATTGTAAAG
Seq A exon
GTGACACTCTAGGGTCTGATTGGGGAGGGGCAATGTGGACATGATTGGGTTTCAGGGACTCCCAGAATCTCCTGAGAGTGAGTGGTGGGTTGCTGGAATGTTGTCTTCACAGTGATGGTTCATGACTCTCATTCTCTAG
Seq C2 exon
CGTGAAGACAGCTGCCTGGACTGTACTGAGTGACAGACGATGTGTTCAGGTCTCTCCTGTGACATCCAGAGCCCTCAGTTCTCTTTACACAACATTGTCTGATGTTCCCTGTGAGCTTGGGTTCAGTGTGAAGAACTGTGGAGCCCAGCCTGCCCTGCACACCAGGACCCTATCCCTGCACTGCCCTGTGTTCCCTTCCATAGCCAACCTTGCTGCTCCAGCCAAACACTGGGGGACATCTGCATCCTGTAAGCTCCATGCTACCCTGAGCTGCAGCTCCTCACTTCCACACTGAGAATAATAATTTGAATGTGGGTGGCTGGAGAGATGGCTCAGCGCTGACTGCTCTTCCAAAGGTCCTGAGTTCAAATCCCAGCAACCACATGGTGGCTCACAACCATCTGTAATGGGATCTAACACCCTCTTCTGCAGTGTCTGAAGACAGCTACAGTGTACTTACATATAATAATAAATAAGTCTTTAAAAAATAATTTGAAAGTGACCTTGATTGTTAACATCTTGATCTAGGGCTGATTTCTTGTTAATTTCATGGATTGAGAATGCTTAGAGGTTTTTTTGTTTGTTTGATTGATTTTTTTGAAGAAATAAATGGCAGATGAAGGAACTTCCAGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000073411:ENSMUST00000172785:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.219 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF077606=DUF1616=PD(6.9=17.9),PF066236=MHC_I_C=PD(48.0=42.9)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGCTCTGAAATGTCTCTCCGAGA
R:
GCAGCAAGGTTGGCTATGGAA
Band lengths:
247-386
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