HsaINT0076824 @ hg19
Intron Retention
Gene
ENSG00000180448 | HMHA1
Description
histocompatibility (minor) HA-1 [Source:HGNC Symbol;Acc:17102]
Coordinates
chr19:1067174-1068743:+
Coord C1 exon
chr19:1067174-1067494
Coord A exon
chr19:1067495-1068412
Coord C2 exon
chr19:1068413-1068743
Length
918 bp
Sequences
Splice sites
5' ss Seq
GGGGTGAGT
5' ss Score
7.93
3' ss Seq
TCCCCTCGGACCTGCCCAAGGAG
3' ss Score
1.41
Exon sequences
Seq C1 exon
GAGCCGCAGGCTGAGGCCGGGAAGGGTCGGGGGCGAGGCCGCGTCGCCGCCTCCCCGAAGCCTTTTCCTGTTGGGGGGAGGGCCCGCCAGTGACGGCCGGGCCTGTCACGTGGGCCTGACAGCTGGGGAGGGGGTGGCCGGCGACAATGTGGTCCCGAAGCGGCCAGCGCCGGGAGCTGCAGCGCTGAGACCCCCAGCCCGCCCCCTCGGGCTCCCGGCCGGGGCCCCATCATGTTCTCCAGGAAGAAACGAGAGCTCATGAAAACCCCTTCCATCTCGAAAAAGAACCGCGCGGGAAGCCCCAGCCCGCAGCCCTCGGGG
Seq A exon
GTGAGTGGAGCCCGGGTGAGACCCGGAGCTGACGCCGGGCCGCAGGGGGACAGGGACCCGCCCTGTGCTCGGGGCTCATGCTGGGGCGGCGGCTGGGGGCTCGTGCCAGCTACAGCCCCTACCGGGCGGGACGGCAGGGGCCACAGCAGAGAGGCCGGGACCCCGGCATTCAGCTCACGGTAGGGACCCTGGGAGTGGTGGCCGCCTCCCTCCACTCCATCCAGGGCTGGCCGCGGGGCCCAGGGAGCAGGAAGGGAGGGTGCCGGGTTGGGACGATGTTGTGTTTGGGCCGCTGCAGGTTGGGGGCTTAGGCAATCTGGGGGCTCTAGGGGCCGTTGAGATGGGAGGGCTGTGGCCTGGCCATTGGGCTGAAGGTTGACCGGGCAGCAGATCCTCTAATGGGATCCACCAGGTTCAGAGGTTGGGGAGTGTCCCCAGGCCTGGGGTGTCTACAAAGCTGGGGGGGGGGTCTACAGAGCTTGGGGGTCCGGGATGTCTACAAGGCCTGGGGCTGCCCATAGGCTCTGGGGTTCCATGGACCTTTAGGGGACAGACAGAGTCAGAAGTGTGTTCACTTAAAGCACCTGCGTTGTAGGAGCCTGAGGGGGGCTTGAAGGGCTGAGGACCCTCCCCACCCCCACCAGGAAGTGGGGACCCCCCTCCCGCGCCTCCCCGCAGGCCCCGCCCCGGCTGTGGTTTGGGCAAGGACCGTTGTTTGTGAAAGCTCTAGGGAAGAGGATGTTGGGTAACAGGTGGGGGGGTACACTACCAAATCTCGGCCCTGTGACCTCTGGCCTTTGACCCCTGTGGGGTCAGGGTGATGGTGGCCCTCCACAGCCCCACTTCATTTCTGGGGAAACTGAGGCCGTGTCCAGGCCGGAAAATCCCTTTAACGAGCTCCCCTCGGACCTGCCCAAG
Seq C2 exon
GAGCTGCCCAGGAAGGATGGGGCTGACGCGGTGTTCCCCGGACCAAGCCTGGAGCCGCCCGCTGGGTCCTCCGGCGTCAAGGCCACAGGGACCCTCAAGCGGCCCACCAGCCTGAGCCGCCACGCCAGCGCGGCTGGCTTCCCCCTGTCGGGTGCTGCCTCCTGGACACTGGGCCGGAGCCACCGGAGCCCACTGACAGCCGCCAGCCCGGGCGAGCTGCCCACCGAGGGTGCCGGCCCGGACGTCGTCGAGGACATCTCCCATCTGCTGGCGGACGTGGCCCGCTTCGCTGAGGGCCTTGAGAAACTTAAGGAGTGTGTGTTGCGTGACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000180448-HMHA1:NM_012292:1
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.574
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CATCTCGAAAAAGAACCGCGC
R:
AAGTTTCTCAAGGCCCTCAGC
Band lengths:
358-1276
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)