MmuINT0078328 @ mm9
Intron Retention
Gene
ENSMUSG00000035697 | Hmha1
Description
histocompatibility (minor) HA-1 [Source:MGI Symbol;Acc:MGI:1917969]
Coordinates
chr10:79479417-79480849:+
Coord C1 exon
chr10:79479417-79479663
Coord A exon
chr10:79479664-79480524
Coord C2 exon
chr10:79480525-79480849
Length
861 bp
Sequences
Splice sites
5' ss Seq
GGGGTGAGT
5' ss Score
7.93
3' ss Seq
TCTTCCCTATGCATACCTAGGAG
3' ss Score
6.38
Exon sequences
Seq C1 exon
ACGTGTGGCTCTGACAGCTGGGGAGGGGGTGGCCCTGAGCAATGTGGTCCAGAGACAGCCTGCACCAGGAGTTGCAGGACTGAGACCACCCCCAGACTCCCACCCTGCCGTTGCCCGCCTGTCCTCACCTAGGGCCACTGGGGCTGACTCCACCATGTTCTCTCGGAAGAAGCGAGAACTTATGAAAACTCCCTCTATTTCCAAAAAGAACCGCGCGGGGAGCCCCAACCCGCAGTCCTCCTCAGGG
Seq A exon
GTGAGTGGGGCACAGAGCGGGTGGGGACCCAGGATGACACCCACAGCCTGTGGTCACTGATGGGCATAGCATGCAACTACAACACCATGCTGGGTCCACGCTGGGGGAACCGGGCCAGCTATAGTCCACACCAGGCAGAATGGCCGGCGACAAGGAGTGGCCTGAACCTAGGAGGCCGCATTACGGTAGGTAGGGATGGCCTTGGGTGGCAACCAAGTCACCCATCTTGATGAGGGATGTCCCCGTCGTGTGCCAATGACGGTTGTGGGTAGTGGGTAGAACTGGTATTGGAGTCTAGTGACTACACTGTAATATGGGGTCTGGGCAATTTTAGGGTTCTGAAAGCCAATGGGGAACTGGTGTTGAACTGGGGTGCAGGTGTACAGAGCAGATTGGGGGGGTCTCCAAGTTTCTCCAGGACCTGCTGCTGCCTGCTGAGCTTTTGAGAATTTGTGAGGTTTAGGGGTACCTCTACTAGGTCTGGGGGTGTCCTGAGACACAGGAGCCTGATGATCTTTTCAGGTCACAGAAGTTATCCATGTTTTTAGAAAGTGGACACCCGTAGAGGTATCTGGGGTGGCTACAGGGTTAGAGACTCACAAGAGTCCTCCCCACCCCCACCAGGAAGTGGGGTGCCCCCTCCCTCCTGTGCCCCACAGGCCCCGCCTCTGGCTGTGGTTTGGGTAGGGACGGTTGTTTGTGAAAGCTATAGACAGGAGGATGTTGGGTAACAGGTGGGGGGGGGGGAGCTTAAAATTCTCTGCCCACTGACCTCTGACCCCTGTGAGGACTTTCTGGGGAAACTGAGGCAGTGTCTGGGATGGGGGATCCCCTTGACTCCTCTTCCCTATGCATACCTAG
Seq C2 exon
GAGCTGCCCAGGAAGGATTGGACAGAAGCTCCCGGCCTGGAGCCACCAGCCACATCCCTGTCCACGGTAGCCAAGGGCACAGGGACACTCAAAAGACCCACCAGCCTGAGCCGCCATGCCAGTGCAGCAGGCTTCCCGCTCTCGGGCACTGCCACCTGGACCCTGGGCCGTGGGTACCGAAGCCCCCTTTCTGCGGCCAGTCCGGCAGAGTTACCCACTGAGGGAGCTTTCCCTGATGGCGTAGAAGACATCTCAACCCTGCTGGCGGATGTGGCCCGCTTTGCTGAGGGCTTGGAGAAGCTCAAGGAGTGTGTGCTGCAGGACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000035697-Hmha1:NM_001142701:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.486
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCTGACTCCACCATGTTCTC
R:
CTACGCCATCAGGGAAAGCTC
Band lengths:
350-1211
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
Other AS DBs: