MmuINT0078330 @ mm9
Intron Retention
Gene
ENSMUSG00000035697 | Hmha1
Description
histocompatibility (minor) HA-1 [Source:MGI Symbol;Acc:MGI:1917969]
Coordinates
chr10:79482420-79483578:+
Coord C1 exon
chr10:79482420-79482543
Coord A exon
chr10:79482544-79483434
Coord C2 exon
chr10:79483435-79483578
Length
891 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGA
5' ss Score
7.66
3' ss Seq
ATGCTAACTCTGCCCGGCAGACC
3' ss Score
6.31
Exon sequences
Seq C1 exon
CCCAGGTCCCTTGACCACGTACTAGCGTTCTGTCCCTCCATACATTACTGAGCAATGTGTGTCTGTGGGACTCTGCATCCAGCGCTGGACCATGACCCCCTGTGCTGCCAGACTCGCGCCCGAG
Seq A exon
GTGAGAGGACAGTGCAGGATGTGGGTCCCCCCACTTAAGGCTAGGACCCTGCACACGTGGCCTGTTCAGGGCCTTGGCACAACCCCAGGGTGCCCAGGAGCTCTTCACCCCTCTTGGCTGCATCTCAGGTTCCATCCTGCCTTGAGGTGGCCCATGTGAGGGGCCGCAGGGACCCCAGCTGCCCAGAGGGTACGTGCCTGGAATGCCCCAGGAGGGGGCGCGGCTTCCCAACCAGAATTCGGGGATTCCTGGATCGGAGTGCAACTCCCGACATGGGCTCAGATTCTGACCACCAAAAACGTGGAGGGAATGGCCTCCGGGGTGGCATTCCACCGGGGCCTTGGTGTCTGCAGGAGGCCAGGGAACTTTTTCAGATTCGGGTTTGAGGAGCTACGGTCTTCAATGTCCTATCATGTCGCATAAGGTCTTGGGCTTGCCTGCACTGTGCAACGGCGGAAAAAACAGTCAAAAATCTCCGCCTTCCAAATGAGGGCCTTTGAGGATGGAGGGCTGTGGTGTGATCTCATAGCGTTGGGGAGGCAGAGGCTGGCCTGAACTGCACAGGGACAGTGTTAAGGCTTGTTCAGCATCTAGATGGGACGCCCGTCCTCTGGCTCTGATGCTTTCCGTGGCTCCCTGCTGCTCAGAGGTATAATGACACAAAAGCCCGGCAAGGTCCTCCTTCCACAGAAAGCTGGGTGACTACTGACAAGTGGCTTTCCCTCACTGTGCACATCTGCAGGGCCAGCGGGGTGTAAGTCCAGGAAAGAGTAAAGTTAATGAACTTGCTTGGGAAAATCGTCTCTTCTGTCCACCCCTGCCTCAGTTTCCCCATCTGGAAAGACTGGGGCCAGCCTCTTCCTTTTCACCCATGCTAACTCTGCCCGGCAG
Seq C2 exon
ACCTTCTCGAGGCCCGCCGGCCACTGGCCCATGAGTGCCTGGGTGAAGCTCTGCGAGTCATGCGCCAGGTCATCTCCAGATACCCACTCCTCAACACCGTGGAGACACTCACAGCCGCTGGTACACTCATTGCCAAGGTCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000035697-Hmha1:NM_027521:1
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCCCTTGACCACGTACTAGCG
R:
CTTTGACCTTGGCAATGAGTGT
Band lengths:
262-1153
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: