MmuINT0078350 @ mm9
Intron Retention
Gene
ENSMUSG00000035697 | Hmha1
Description
histocompatibility (minor) HA-1 [Source:MGI Symbol;Acc:MGI:1917969]
Coordinates
chr10:79485020-79487596:+
Coord C1 exon
chr10:79485020-79485100
Coord A exon
chr10:79485101-79487407
Coord C2 exon
chr10:79487408-79487596
Length
2307 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGG
5' ss Score
9.68
3' ss Seq
GATCCTCTCTCCTCTCACAGCAA
3' ss Score
9.91
Exon sequences
Seq C1 exon
CCCCTGACGCTGCGGCGGTTGGAGCATGAGAGGCGCAGGAAGGAGATCAAAGAATCTTGGCATCGAGCACAGAGGAAGCTG
Seq A exon
GTAAGGGCAGCGGGGGTTGTGGCCAGTGCCCCCCTCGTTGGTCGATGCAGGTTCCCTGTGCTTGCAAGAGCAGTCATTGCTGAGATGCTGAGACAACCAGCCCCAGCAGGGCACTCAAGAGTCCCACACATTGTCAGCTGTTCAGAAATTCGGAGAGAAAAGAGTGCAGTCCCCGCCTCGGTTGGTGCACACTCCATGTACCCCATTTTTCTTTTGGGGCATTTAAAGGCATGGAGGTGGCCTGGGGGGCATGCCTCAGTGGGTAAAGCACCTGACAGGAGAACATGGGGTCCTGAGTCACGGGGTTAGCATCCCCATAAAACCAGGAATGGCAGCCAGGCGAGGTGGCACACGCCTTTAATCCCAGCACTCAGGAGGCAGAGGCAGGTGGATTTCTGAGTTCGAGGCCAGCCTGGTCTACAGAGTGAGTTCCAGGATAGCCAGGGCTACACAGAGAAACCCTGTCTCGAAAAACCAAGGCGGGGGGGACAAAAACCAGGCATGGCATCCTGCACCTGGAACCCCAGCACCCAACCCAGGTGGGATGGGTGGTTCTCGGGCTCCATAGCCAGAAAGCCTAACTGAATCTGGGCTCACTGGGACACCTGTCTCAGAAAACAAGATGTGTGTGGGGGTGTGGCCGGTAGTGGTGCCTGCCTTTAATCCTAGTACTCGGGAGGCAGAGGCAGGAGGCTCTCTGTCCTGGTCCAGTCAGGGCTGCATAGTGAGGCTCTGCCTCAAAACTGACAGATACACAGCAGACAGAGATGGTGTCCAGCCTCACGGTAACAAGCCTGCGCCCCCCACCCCTGTCTCTGATTGGAGTTCGAAAATGAATGAGTCATTGGGGGCAGGCACCTGCTTCCCTCGCAGCTCCAGCCCCTCTTCTCAGTTTCTGTGAATCCTCTCTGTCTATATTCTCTGCTCAGAGTAGATGACACAGGGGATTGTTATTGATTTCCGAGAGCTCTGTACATATTATGGAATACAAACTACAATACTGTTGGGAGTCCCTCCCTCAAATTTTGTCATTTGATACTTTAATTGTACTAATTTGACATTTTTTAAAAAGCTATCAGGACAGGCTGGTGGGAACTGTTTAGTTTTAACACTAGGAGGCAGAGGCAGGCAGATCTCTGGGAGTTCAAGGCCAGCCTGGGTTACATAGTGAGTTCAGGATAGCGAGAGCTGTGTAGAAAGACCTTGTCTAAAAAAAAAAAAAAAAAAAAAAAAAGCCAGTAGAGTTTTCAGATATTGTTTACAGTTGTTTGCTTAGTGGGTGGGTGGGGATGGAAATGCCACAGCGTTATCGGGAGGTCAGAGAACAGCTGGTGGAGGTGAGTTCTCTCCTTCCACCATGCGGGCGCAGGGATTGGATTGAGGTCCTTCGGCTTGGGGACAAGTGCCTCTACCCACCCAGACAGTGGTTCTCAGGCTTCCTATTCCTAATGCAGCCTGCGACCCTATAATAAATACAGCACATGTTGTGCTGGCCCACAGCCATGAATTTGATGTGTTGCTGCTTCATAACTAATTTTGCTACTGTTATGAATCATGATATCTGATATGCTGCTCCCCGACCTAAAGGGGTCGTGACCCACAGGTTGAGAACCGCTGTGCTGGCAGCAGCAGCTCCTAGCTTTGCTGTGAGGACTATCTGTCTGTCTGTCTGCCTGTCTGTCTGTCTATTTGTATTTTGGGTTTTTCGGGGCAACATCTCTGTGTAGTCCTGGTTGTCCTGGAACTTGCTCTGTAGACCTGGCAGGCCTTGAACTCCCAGAGATCCACCTGCCTCTGCCTTCCTAGTGCTGGGATTAAAGGTGTGCACCACTGCCTGGCTTGAGGTTTGTTTGTTTGTTTTGAGAATCCAGGCTTAATGTGAGCTCTTCCTCTGAGACCCTGGAGTATCCCCTACAGTCCCTATTCTTCATGTCTAGGTTCTGACTTTCAGACTGTGGGGTGTGGGCTCTCCCCACCCAGACCAGTTACTTTGTGACTCAGTGCTTCCTGTCACCCCAGGGTGCTAGGCTTCCTGCCTGGGCGGCTCTCTGTTTTCATCTGTAAGACAGGAAGTGAAACTTACCGAGACCAGGCATGGGGAGAGGGGAGATGTGTTTCAGTTTGTGTTTTTTGTTCAGCTCTGAGTCGTGCCTCAGTTTCCCCGTGGGGTCCTACTGCAGATGCTGCCAGTGTGTGCTGTCAATGGTCCCCTGCTGGCTTGCTGGGAATGTGGGGTCCTTGCTGGTGAGGAGGGAGGGTGTGCAGAGCCAGGGTGAGGCACAAGCTGGATCCTCTCTCCTCTCACAG
Seq C2 exon
CAAGAGGCAGAGGCCAACCTGCGCAAGGCCAAACAGGGCTACAAACAACGCTGTGAAGACCACGACAAGGCCCGGCTCCAGGTGGCCAAGGCTGAGGAGGAACAACAGGGCACAGGCCCAGGCGCAGGGACTGCGGCCTCTAAGGCCCTGGACAAGAGGCGCAGACTGGAGGAAGAGGCCAAAAACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000035697-Hmha1:NM_027521:9
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.968
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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: