HsaINT0076842 @ hg19
Intron Retention
Gene
ENSG00000180448 | HMHA1
Description
histocompatibility (minor) HA-1 [Source:HGNC Symbol;Acc:17102]
Coordinates
chr19:1073947-1074240:+
Coord C1 exon
chr19:1073947-1074013
Coord A exon
chr19:1074014-1074102
Coord C2 exon
chr19:1074103-1074240
Length
89 bp
Sequences
Splice sites
5' ss Seq
CCGGTAAGC
5' ss Score
8.8
3' ss Seq
CAGGCCCCCGTTCCCTGCAGGCT
3' ss Score
8.7
Exon sequences
Seq C1 exon
TCCATGGAAAGCCTGTATGGACCGGGCAGTGAGGGCACGCCTCCCAGCCTGGAAGACTGTGACGCCG
Seq A exon
GTAAGCCCCCACCCAGCGGCAGGCAGGCATTTGAGGGGTGGGCCATTGCGCGGGTCGGGCCAGGCTGAGCAGGCCCCCGTTCCCTGCAG
Seq C2 exon
GCTGCCTGCCCGCCGAGGAGGTGGACGTGCTGCTACAGCGCTGTGAGGGGGGCGTGGATGCCGCACTGCTGTATGCCAAGAACATGGCCAAGTACATGAAGGACCTCATCAGCTACCTGGAGAAGCGGACGACGCTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000180448-HMHA1:NM_012292:6
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.826 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0061118=FCH=PU(42.1=85.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Cow
(bosTau6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGAAAGCCTGTATGGACCGG
R:
CCAGGTAGCTGATGAGGTCCT
Band lengths:
183-272
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)