HsaINT0076838 @ hg19
Intron Retention
Gene
ENSG00000180448 | HMHA1
Description
histocompatibility (minor) HA-1 [Source:HGNC Symbol;Acc:17102]
Coordinates
chr19:1084237-1086627:+
Coord C1 exon
chr19:1084237-1084345
Coord A exon
chr19:1084346-1085658
Coord C2 exon
chr19:1085659-1086627
Length
1313 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGT
5' ss Score
10.03
3' ss Seq
CATCTGTCTCCCTTTCTTAGAAT
3' ss Score
10.47
Exon sequences
Seq C1 exon
GACGAGTCATCCAACCAGCGAGCTGAGGTAGTCGTCCAGGTGCCGTACCTGGAGGCGGGCGAGGCGGTGGTCTACCCGCTGCAGGAGGCGGCGGCGGACGGGTGCAGAG
Seq A exon
GTGAGTGTGTGGCTGCCCGAACGGCCCCAAGGGAGGCTGGCGTGTGCCACCCATGGGCGCAGGTGCCATGACCTAGTTGTACACACGTGGCAGGGTCCACGGTGCTGCACATTCTGTGGATTTCGTCTGCCACGGAGACCACACCTATGAGCTACTCATTCAGTGTCCTTTAACCGGCTGCAAAAACAGGCAAGGCAGTGCCTTTTGAGGTGCCTACCCCGCACTCAGAAACCAGTAACGTGAACGTGGGGCTGATGCCTTGTGAGGCTCCAGGTGCACCAGGTCAGGCTAAGTGCCTTTCCTGCAGGAGCCCGTTTTTCTAGAGAAGGGCGTGGGGCTGGGAGTTTGACCCACGTGGGGCCAGCACCACCTGTCAGAGGCAGCTGGCCGAGTGCCGCATCTAGTTATGGGACACCTGTGTTGTCTGTCTTCACACTGCTGATAAATAAATACCTGAGGCTGGGCACGGTGGCTCACGCCTGTAATCCTCGCACTTTGGGAGGACAAGGCAGATCACTTGAGGTTAGGAGTTCAAGACCAGCCTGACCAACATGGTGAAATCCCATCTCTACTAAAAATACAAAAATTAGACAGGTGTGGTGGAGGGCACCTGTAATCCCAGCTACTCAGGAGGCTGAAGCAGGAGAATCACTTGAACCGGGGAGGCAGAGGTTGCACTGAGCCAAGATCATGGCACTGCACTCCAGCCCGGGCAAGAGAGAGAGACTCTGTCTCAAAAAGAAATACCTGAGACTGGGCAATTTACAAAAGAAAGAGGTTTAATGGAGTTACAGTTCCATGTAGCTGGGGAGGCCTCACAATCATGGCAGAAAGCAAAGAGGAGCAAGTCACATCTTGCATGGATGGTGGCAGGCAAAGGGAGAGCTTGTGTCCGGAAACTCCAGTTTTTAGACCATCAGATCTTGTGAAACCCACGTACTATCATGAGAACAGCCCAGGAAAGACGCACCTCCAGGATTCAACCATCCTCCACCAGCTCCCTCCCACAACACGTGGGAATTATGGGAGCTACAAGATGAGGTTTGGGTGGGGACACAGAGCCAGACCCTATCAACACCTCTCTCCTTCCGTTTCTCCCCTTGTCTCTCTCTCCTCCTCCCCGCCATGTCTCTCCATCTGTCTGTCCCTCCCCTTGTCTCTCCTCCATCTCTCCTGTCTCTCCCCATCTCTCCTGTCTCTCCATCTCTCTCCCCCCTCTCCTGTCTCTCCCCATCTCTCCTGTCTGTCCCTCCCCTTGTCTCTCCTCCATCTCTCCTGTCTGTCTCCCCCCGCCATCTGTCTCCCTTTCTTAG
Seq C2 exon
AATCCCGAGTTGTGTCCAACGATTCGGACTCGGACCTAGAGGAGGCCTCCGAGCTGCTGTCCTCATCGGAGGCCAGTGCCCTGGGCCACCTCAGCTTCCTGGAGCAGCAGCAGAGCGAGGCCAGCCTAGAGGTGGCTTCTGGCAGCCACAGCGGCAGTGAGGAGCAGCTGGAGGCCACAGCCCGGGAGGACGGGGACGGGGACGAGGACGGCCCGGCCCAGCAGCTCTCAGGATTCAACACCAACCAGTCCAACAACGTGCTGCAGGCCCCACTGCCCCCCATGAGGCTCCGTGGCGGGCGGATGACACTGGGCTCCTGCAGGGAAAGGCAGCCGGAATTCGTGTGAGCTGGGGTGGGGCTGGGACCACAGGTGGCTTCTCTCTTGCCTGCTCCTGTCCCTCCAGCACGTCCCCTGCACCACGGCATAGCTTAGGTGCGCCGTCCTGGGGTCGCTGCCGAGAGCGCCTGGACTTCGACGTCCCACCAGCGGGCGCCTCCTCCCAGAGGCTTCCAGGAGCACGAGGGCCTTGCGGCACAGGACTGTGCCCTGTGCTGTCCCCTGCACCCCGGCTCAGCTGAGCTGGGGAACACTGCTGTCGTGTGAAGTCACAGTGGCCTTGTTGGTGCCCACAGGGCTGTGTGGATGGAGGAAGCTGTCCCTGCCCAGTGCATCCCCCAGGTCATCACGGGGACGCAGGAGGCAGGCCCTGCCCTGCCCTCTCCTCACAGGTCTGTTGCAGGGACTCCAGAAACCATTCTGGGAGCCGTGGATGGGGGCGGAGCTGGGGTTTGGTGCAGTTTCCAGGGTGCAGTACAGCAGGGCCTGAATACTGGCCCTGGACTCCCTTTTCCAGAACACCAGGTGTGGCCACCTGGGGCTCAGGTACACAGTGGGGTCTCTCGGAAGCCACCGTGTGGTTCTTTCACAGGCACGTTTATTTTGCTGAAATAAAAAGTTTTTAATCGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000180448-HMHA1:NM_012292:22
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.459 A=NA C2=0.925
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGCTGAGGTAGTCGTCCAGG
R:
CGTTGTTGGACTGGTTGGTGT
Band lengths:
348-1661
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)