HsaINT0076832 @ hg19
Intron Retention
Gene
ENSG00000180448 | HMHA1
Description
histocompatibility (minor) HA-1 [Source:HGNC Symbol;Acc:17102]
Coordinates
chr19:1080891-1081737:+
Coord C1 exon
chr19:1080891-1081063
Coord A exon
chr19:1081064-1081548
Coord C2 exon
chr19:1081549-1081737
Length
485 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGT
5' ss Score
10.03
3' ss Seq
CTCACTCTGGCCGCCCCCAGTGC
3' ss Score
7.65
Exon sequences
Seq C1 exon
CTGACCTCAACGGCATGACCCCCGAGCTGCCGGTGGCCGTGCCCAGTGGACCGTTCCGCCACGAGGGGCTGTCCAAGGCGGCCCGTACTCACCGGCTCCGGAAGCTCCGCACGCCCGCCAAGTGCCGCGAGTGCAACAGCTACGTCTACTTCCAGGGTGCTGAGTGTGAAGAG
Seq A exon
GTGAGTGGGACGCCCCGACGGACAGCTGGGAGCCTTCGGGAGCCTTTGGGGTGCCCAGCACCGCCGGCCTGTGTGCCCTCAGGAATGTCCGGCCCAGAGCAGGGAGCAGTCGGACGCCTTTGGAAGGAAGCGAACGGAGGGGGTGGGGTGGGCTCTTTTAGTTCTGGGGAGCAGGGTTGGCTCTCTGAGGCAGCGAGGCAGGGGGCAGACCTGGAGGGTGAAGAGTCCTGGGGCTGTGGCCAGAAGACCTGGAGGGCAAAGGCCCTGGAGCTGTGTCCAGAAAACCAAGGGGCGGGAAGGAGAGGAGGCCACAGGGCAGGCGGGATCACCCCTGGGGTGGAAGCCACGAGCCACTGTCCAGCTTGTGTTTGCAGAAGCTGCCGTGTGGGGGCTGTGAGCGCCCCGGGGAGGTGGGGTGGAGCCGCTGGGGGCTGCGCTGAGCTGGGCGCCCCGGGGCTGGGCTCACTCACTCTGGCCGCCCCCAG
Seq C2 exon
TGCTGCCTGGCCTGCCACAAGAAATGTCTGGAGACGCTGGCCATACAGTGCGGGCACAAGAAGCTGCAAGGCCGCCTGCAGCTGTTCGGCCAGGACTTCAGCCACGCGGCCCGCAGCGCCCCCGACGGCGTGCCCTTCATCGTCAAGAAGTGCGTCTGCGAGATCGAGCGGCGGGCGCTGCGCACCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000180448-HMHA1:NM_012292:17
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.517 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0013017=C1_1=PU(57.1=48.3)
A:
NA
C2:
PF0013017=C1_1=PD(38.8=30.2),PF0062022=RhoGAP=PU(10.4=28.6)
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:
CTGACCTCAACGGCATGACC
R:
GCTCGATCTCGCAGACGC
Band lengths:
342-827
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)