HsaINT0076829 @ hg19
Intron Retention
Gene
ENSG00000180448 | HMHA1
Description
histocompatibility (minor) HA-1 [Source:HGNC Symbol;Acc:17102]
Coordinates
chr19:1080254-1080546:+
Coord C1 exon
chr19:1080254-1080378
Coord A exon
chr19:1080379-1080462
Coord C2 exon
chr19:1080463-1080546
Length
84 bp
Sequences
Splice sites
5' ss Seq
GGGGTGAGT
5' ss Score
7.93
3' ss Seq
AGAGACGCCTCTTTCTCCAGCCG
3' ss Score
4.08
Exon sequences
Seq C1 exon
GTCCCCCGTCATGCGTGCCCGGAAGAGCAGCTTCAACGTGAGTGATGTGGCGCGGCCGGAGGCTGCCGGGAGCCCCCCAGAAGAAGGCGGGTGCACTGAGGGCACACCTGCCAAGGACCACAGGG
Seq A exon
GTGAGTGTCCGGCGGGGCCCAGGGGCGGACGCTGGCTCCCTGCGACCCACCCTGGCCCTTCACCAGAGACGCCTCTTTCTCCAG
Seq C2 exon
CCGGGCGAGGACACCAGGTTCACAAGTCATGGCCGCTCTCGATCTCAGACTCGGACAGTGGGCTGGACCCCGGCCCTGGCGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000180448-HMHA1:NM_012292:14
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.814 A=NA C2=1.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAGAGCAGCTTCAACGTGAGT
R:
AGCCCACTGTCCGAGTCTG
Band lengths:
167-251
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)