HsaINT1015537 @ hg38
Intron Retention
Gene
ENSG00000204525 | HLA-C
Description
major histocompatibility complex, class I, C [Source:HGNC Symbol;Acc:HGNC:4933]
Coordinates
chr6:31268749-31269385:-
Coord C1 exon
chr6:31269338-31269385
Coord A exon
chr6:31269174-31269337
Coord C2 exon
chr6:31268749-31269173
Length
164 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGA
5' ss Score
8.68
3' ss Seq
ATGACTATTGTGTTCTGTAGCCT
3' ss Score
6.43
Exon sequences
Seq C1 exon
GCAGCAACAGTGCCCAGGGCTCTGATGAGTCTCTCATCACTTGTAAAG
Seq A exon
GTGAGATTCTGGGGAGCTGAAGTGGTCGGGGGTGGGGCAGAGGGAAAAGGCCTGGGTAATGGGGATTCTTTGATTGGGACGTTTCGAGTGTGTGGTGGGCCGTTCAGAGTGTCATCGCTTACCATGACTGACCTGAATTTGTTCATGACTATTGTGTTCTGTAG
Seq C2 exon
CCTGAGACAGCTGCCTGTGTGGGACTGAGATGCAGGATTTCTTCACACCTCTCCTTTGTGACTTCAAGAGCCTCTGGCATCTCTTTCTGCAAAGGCACCTGAATGTGTCTGCGTTCCTGTTAGCATAATGTGAGGAGGTGGAGAGACAGCCCACCCCCGTGTCCACCGTGACCCCTGTCCCCACACTGACCTGTGTTCCCTCCCCGATCATCTTTCCTGTTCCAGAGAGGTGGGGCTGGATGTCTCCATCTCTGTCTCAAATTCATGGTGCACTGAGCTGCAACTTCTTACTTCCCTAATGAAGTTAAGAACCTGAATATAAATTTGTGTTCTCAAATATTTGCTATGAAGCGTTGATGGATTAATTAAATAAGTCAATTCCTAGAAGTTGAGAGAGCAAATAAAGACCTGAGAACCTTCCAGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000204525:ENST00000376228:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF126692=P12=PD(25.0=82.4),PF066236=MHC_I_C=PD(51.7=88.2)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Cow
(bosTau6)
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:
CCAGGGCTCTGATGAGTCTCT
R:
GGAAAGATGATCGGGGAGGGA
Band lengths:
252-416
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains