MmuINT0075595 @ mm9
Intron Retention
Gene
ENSMUSG00000016283 | H2-M2
Description
histocompatibility 2, M region locus 2 [Source:MGI Symbol;Acc:MGI:95914]
Coordinates
chr17:37617796-37619703:-
Coord C1 exon
chr17:37619428-37619703
Coord A exon
chr17:37618693-37619427
Coord C2 exon
chr17:37617796-37618692
Length
735 bp
Sequences
Splice sites
5' ss Seq
CAGGTACGA
5' ss Score
10.03
3' ss Seq
ATCCTACTCTTCCTCCTCAGAGC
3' ss Score
9.75
Exon sequences
Seq C1 exon
GTTCTCACACCATCCAAAGGATGACTGGCTGCTACATTGGACCAGACGGGCACCTACTTCACGCATACCGTCAGTTTGGTTATGATGGGCAAGATTACCTCACTCTGAATGAAGATCTGAGCACCTGGACTGCAGCAGATGCGGCAGCTGAGATCACCCGTAGAGAGTGGGAGGCAACTAATGTGGCTGAGTTCTGGAGGGTCTACTTGGAGGGCCCTTGCATGGTGTGGCTCTTTAAATACCTGACAGTGGGAAATGAGACTCTACTGCGCACAG
Seq A exon
GTACGAGGGGCAAAGAAGTAACTCCTCTTAATGAACTGGAGCTCATGTCTCCTGAGAAGGGAGAAATGGGATCAGCTAGAATTCTCTGTGTATCTGTCTCTCTGACTCTGTCTCTATGTGTCTCTTTGTTTCTGTCTCCCTAGCTCTGCCTCTCTGTGTTTCTGTCTCTCTGTCTCACCTCTCACCTCTCTCTGTGCCCTCCTCCTCCCTCTCTTACACACACACACACACACACACACACACACACACACACACACACACCTTGAGAAGGAAGAATGATCCTGAGTTTCCTGGTTCAACATCATAGGACGTCTCTCCAGAGGACTCACTCTTCTCTCCAAGTCTCAGTTCAGAATCTATCTCAGAATAGGAGAAAAGATCCCTAAACTTGCTATTCCCTTCAATCTGCAGCCTGTACCCTCTCTGAGGTTAGATTCTCTGACCACACTCAATGGTATGATACGGCTGCAGTGATGTAGTTTCTTGGCTTCACTCAGTCAGGACAAAAGTTGCTCTTTTCCTGGTAACCCAGCGTCTCCTACCCTAGGCTAGGTCACCTTGATTCTAGAACTTTTCAAGCAGTTTATTATCCCAGATGCTTGAGTACAGTTGCTATGTAGGTCTGCACATATCCCCACCCTATTCCCCTGTCTAGTCCCAAAATGATCACAATAACACCAAATCCAAAGGGGGAAAAAAAGTAAATGTACTACTTATCCTACTCTTCCTCCTCAG
Seq C2 exon
AGCCCCCAAAGGCATATGTGACCCATCACCCCAGACCTGAAGGTGATGTCACCCTGAGGTGCTGGGCCCTGGGTTTCTACCCTTCTGACATCATCATGATCTGGCAAAGAGATGGGGAGGACCAGACCCAGGACATGGATGTTATTGAGACCAGACCTGCAGGGGATGGAACCTTCCAGAAGTGGGTAGCTGTGGTGGTGCCTTCTGGGAAGGAGCAGAATTACACATGCCATGTGGCTCATGAGGGACTGCCTGAGCCCCTCACCCTGAGATGGAGTAAGTAGGATGTAGGCACATAGCCTGTGGTTAGAGAAGGCAAAAGCCTTTCTGGAGATCCTGAGCAGGGTCAAGGTTGAGATCTGGGGTCAGGGTCCTACAATTTTACATTTCTTTTCAGGTAGACCTCCTCAGTCTTTCATTTTCATCATAATAGTTGCTGTTGGCCTGGTTCTCCTGGGAGCTTCAGTGGCTACTCTTGTCATGTGGAAGAAGAGCTCGGGTGGGGAAAGGGGCAGCCTCTGATTTTTTTTTTCCAACTGAGAGACTCTAAGCCCCAGATAAGTTTTCTCTGCCTCCTTGTTGGGAAGGAGTGTGGCCCATTATTCCCAAAGACACAATTCTGAATGTCATAACTGAAACATTTTAATCTCAAAAAATCAAAATCCCCAAAATACATTTAAAAAAGAAATACAAAAAAAAGGGAAAAAAGTATCCAAACCATAAGATAGATTTAAAGGGATATTTATACACACACACAAGAAAAGGAAAAAGAAAAAGAAGAAAAAGGAAACGAAGAAAAAGAAAAAGGAAAGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGAGAAATCACGATAGAAGAGGGGTCTCTGTATGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000016283-H2-M2:NM_008204:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.156
Domain overlap (PFAM):
C1:
PF0012913=MHC_I=PD(49.2=94.6)
A:
NA
C2:
PF0765410=C1-set=WD(100=87.4)
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:
GGCACCTACTTCACGCATACC
R:
GTCTGGTCCTCCCCATCTCTT
Band lengths:
355-1090
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: