HsaINT0076841 @ hg19
Intron Retention
Gene
ENSG00000180448 | HMHA1
Description
histocompatibility (minor) HA-1 [Source:HGNC Symbol;Acc:17102]
Coordinates
chr19:1073673-1074013:+
Coord C1 exon
chr19:1073673-1073745
Coord A exon
chr19:1073746-1073946
Coord C2 exon
chr19:1073947-1074013
Length
201 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
CCTGCGTCTCCGTCCTACAGTCC
3' ss Score
9.52
Exon sequences
Seq C1 exon
AGTGTCCGAGTTCCTCATGGGTGAAGTGGACAGCAGCACCCTCCTAGCAGTGCCTCCTGGGGACTCGAGCCAG
Seq A exon
GTGAGTGGGGTGGGCCAGGGCCACCTGTGTCCAGCTTCTGGAGGCCAGCCGGGTTCAGGTCTGCAGGGCCCAGACAGTCACCCTGCTTCCCCTGTGCGCCTTGGTTTCCCTCTCTGGGGGAGGCAGCAACCGTCCCCTGAAGGGTGGGCACTGCCCAGGGCCCCGCATGGGGCTGGTCTCACCTGCGTCTCCGTCCTACAG
Seq C2 exon
TCCATGGAAAGCCTGTATGGACCGGGCAGTGAGGGCACGCCTCCCAGCCTGGAAGACTGTGACGCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000180448-HMHA1:NM_012292:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.120 A=NA C2=0.826
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
Cow
(bosTau6)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGTGTCCGAGTTCCTCATGGG
R:
CGGCGTCACAGTCTTCCAG
Band lengths:
140-341
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)