HsaINT0076479 @ hg19
Intron Retention
Gene
ENSG00000237218 | HLA-H
Description
major histocompatibility complex, class I, H (pseudogene) [Source:HGNC Symbol;Acc:4965]
Coordinates
chr6:29858041-29858856:+
Coord C1 exon
chr6:29858041-29858073
Coord A exon
chr6:29858074-29858215
Coord C2 exon
chr6:29858216-29858856
Length
142 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGT
5' ss Score
10.08
3' ss Seq
CTGTTTTTATTCTACTCGAGGCA
3' ss Score
3.95
Exon sequences
Seq C1 exon
ATAGAAAAGGAGGGAGCTACTCTCAGGCTGCAA
Seq A exon
GTAAGTATGAAGGAGGCTGATCCCTGAAATCCTTTGGATATTGTGTTTGGGAGCCCATGGGGGAGCTCACCCACCCCACAATTCTTCCTCTAGCCACATCTACTGTGGGATCTGACCAGGTCCTGTTTTTATTCTACTCGAG
Seq C2 exon
GCAGCAACAGTGCCCAGGGCTCTGATGTGTCTCTCACGGCTTGAAAGGTGAGACCTTGGGGGGCCTGATGTGTGGGGGATGTTGGGGGGGAACAGTGGACACAGCTGTGCTATGGGGTTCTTTGAATTTGATGTTTTGAGCATGCGATGGGCTGCCAAAGTGTCATCCATTACTGGGACAGATATGAATTTGTTCATGAATATTTTTTCTATAGTGTGAGACAGCTGCCTTGTGTGGGACTGAGAGGCAAGAGTTGTTCCTGCCTTCCCTTTGTGACTTGAAGAACCCTGACTTTCTTTCTACAAAGGCACCTGAATGTGTCTGTGTTCCTGTAGGCATAATGTGTGGAGGAGGGGAGACCAACCCACCCTCATGTCCACCATGACCCTCTTCCCCACGCTGATCTGTGTTCCCTCCCCAATCATCTTTCCTGTTCCAGAGAGGAGGGGCTGAGATGTCTCCATCTTTTTCTCAACTTTATGTGCACTGAGCTGTAACTTCTTACTTCCCTCTTAAAATTAGAATCTGAGTAAACATTTACTTTTTCAAATTCTTGCCATGAGAGGTTGATGACTTAATTAAAGGAGAAGATTCCTAAAATTTGAGAGACAAAATAAATGGAACACATGAGAACCTTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000237218-HLA-H:NR_001434:6
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=NA
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NA
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
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:
GAGGGAGCTACTCTCAGGCTG
R:
CACAAGGCAGCTGTCTCACAC
Band lengths:
258-400
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
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)