HsaINT0076836 @ hg19
Intron Retention
Gene
ENSG00000180448 | HMHA1
Description
histocompatibility (minor) HA-1 [Source:HGNC Symbol;Acc:17102]
Coordinates
chr19:1082839-1083352:+
Coord C1 exon
chr19:1082839-1083065
Coord A exon
chr19:1083066-1083141
Coord C2 exon
chr19:1083142-1083352
Length
76 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
GGCCCCTGCCCACCCCGCAGGAT
3' ss Score
8.16
Exon sequences
Seq C1 exon
CTTCCCGAGCCGCTCATCTCCTTCCGCCTCTACCACGAGCTCGTAGGGCTGGCCAAGGACAGCCTGAAGGCAGAGGCCGAGGCCAAGGCGGCGTCCCGGGGCCGGCAGGACGGCTCGGAGAGCGAGGCAGTGGCGGTGGCCCTGGCAGGTCGGCTGCGGGAGCTCCTGCGGGACCTGCCGCCTGAGAACCGGGCCTCGCTGCAGTACCTGCTGCGTCACCTACGCAG
Seq A exon
GTGAGTCCCGGCATATGGAGTGGAGGGCGCGGGGTCCCGGGAGCCGCTCAGCACCTGGCCCCTGCCCACCCCGCAG
Seq C2 exon
GATCGTGGAGGTGGAGCAGGACAACAAGATGACCCCCGGGAACCTGGGCATCGTGTTCGGGCCCACGCTGCTTCGGCCACGGCCCACCGAGGCCACCGTGTCCCTCTCCTCCCTGGTGGATTATCCCCATCAGGCCCGCGTCATCGAGACTCTCATCGTCCACTACGGCCTGGTCTTCGAGGAGGAGCCGGAGGAGACCCCCGGGGGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000180448-HMHA1:NM_012292:20
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.132 A=NA C2=0.211
Domain overlap (PFAM):
C1:
PF0062022=RhoGAP=FE(43.4=100)
A:
NA
C2:
PF0062022=RhoGAP=PD(18.5=45.1)
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:
CAGTACCTGCTGCGTCACCTA
R:
GATGACGCGGGCCTGATG
Band lengths:
171-247
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)