HsaINT0076834 @ hg19
Intron Retention
Gene
ENSG00000180448 | HMHA1
Description
histocompatibility (minor) HA-1 [Source:HGNC Symbol;Acc:17102]
Coordinates
chr19:1081823-1083065:+
Coord C1 exon
chr19:1081823-1081960
Coord A exon
chr19:1081961-1082838
Coord C2 exon
chr19:1082839-1083065
Length
878 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGA
5' ss Score
9.22
3' ss Seq
TGACCCTTGACTCTGCGCAGCTT
3' ss Score
6.33
Exon sequences
Seq C1 exon
GGCATCTACCGGGTCAATGGGGTAAAGACACGCGTGGAGAAGCTGTGCCAGGCCTTCGAGAACGGCAAGGAGCTGGTCGAGCTGTCGCAGGCCTCGCCCCACGACATCAGCAACGTCCTCAAGCTCTACCTGCGTCAG
Seq A exon
GTGAGACCCACCGGTGGTGGCCAGGCAGAGCCTGGAAGGGGCGTAGCCAGGCAGGAGGAGGCGGGGTGGGGGTCCGGGAGCTGGAGCAGGACTGAGCTGGAGCAGGACTGGCGCAAGCGGGGGCCTGGGGAGGACAGGGTGGGCGGGACAGTGCCTGGCAGGGCAGGGCTGAGGCTGGGGGCGTGGTCACGGTAGGAGCGAGGCGGGGCCAGTTCTGCGCCGAGGCACGGACAGGGACAGGAGGGGCGGGGTGGGGCTTGGTCAGCACGTGGCAGGGGTGTGGCCACGGCAGAGGCACACCTGACGCTGTGCGGGGGCGGGGCCGGGGCCGGGGCTCGGTGGGGCGTGGCCAGAGCAAGATGGGCGTGTTCAGCGCTTGGCAGGGACCCGTATGAGGCTAGGGGCGGGGCTGAGGCTAGACAAGTGCGGGGCTGGCGGTGGGGCCTGGGCTTGGTGGGGCGAGGCTGGGGCCAGGGGCGTGGTCATCCCCGGGGAAGGGCGGGACTGGGGCTAGGGGCGTGGTCATGTCTGGGGAAGGGCGGAGCTGGGCTGGGATGGGAGTGGGACCAGCACTTCGCAGGTGGTTGGGAAGGGGTCAGACTATGCTGAGTGGAGCCGGAGCTCGTTAGGGTACCTGCAGGGCGGGGCGCGCGTGGCCAGAGCGAGAAAGGGAGTGGAGCTGCGGGCGTGGCCCGGGTAGGAGGGGCAGGGCTCACGCTGGGCTGGGAAAGGGGACTGACGCCGCTCTGGGTGGAACCCGAGCTCGGTGGGGTGTGGCCAGTGCTCTGTGGGGGTGGGGCTGAGGCTGGGGGCGTGGCAGGCACACGTGGGGGCTGGGCCAGGCCCACCAACACCTGCTGACCCTTGACTCTGCGCAG
Seq C2 exon
CTTCCCGAGCCGCTCATCTCCTTCCGCCTCTACCACGAGCTCGTAGGGCTGGCCAAGGACAGCCTGAAGGCAGAGGCCGAGGCCAAGGCGGCGTCCCGGGGCCGGCAGGACGGCTCGGAGAGCGAGGCAGTGGCGGTGGCCCTGGCAGGTCGGCTGCGGGAGCTCCTGCGGGACCTGCCGCCTGAGAACCGGGCCTCGCTGCAGTACCTGCTGCGTCACCTACGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000180448-HMHA1:NM_012292:19
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.132
Domain overlap (PFAM):
C1:
PF0062022=RhoGAP=FE(26.0=100)
A:
NA
C2:
PF0062022=RhoGAP=FE(43.4=100)
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:
TCAATGGGGTAAAGACACGCG
R:
GTAGGTGACGCAGCAGGTACT
Band lengths:
348-1226
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)