HsaINT0076440 @ hg19
Intron Retention
Gene
ENSG00000206435 | HLA-C
Description
major histocompatibility complex, class I, C [Source:HGNC Symbol;Acc:4933]
Coordinates
chr6:31237987-31239125:-
Coord C1 exon
chr6:31238850-31239125
Coord A exon
chr6:31238263-31238849
Coord C2 exon
chr6:31237987-31238262
Length
587 bp
Sequences
Splice sites
5' ss Seq
CAGGTACCA
5' ss Score
7.88
3' ss Seq
TTTCTGACTCTTCCCGTCAGAAC
3' ss Score
7.9
Exon sequences
Seq C1 exon
GGTCTCACACCCTCCAGAGGATGTCTGGCTGCGACCTGGGGCCCGACGGGCGCCTCCTCCGCGGGTATGACCAGTCCGCCTACGACGGCAAGGATTACATCGCCCTGAACGAGGACCTGCGCTCCTGGACCGCCGCGGACACCGCGGCTCAGATCACCCAGCGCAAGTTGGAGGCGGCCCGTGCGGCGGAGCAGCTGAGAGCCTACCTGGAGGGCACGTGCGTGGAGTGGCTCCGCAGATACCTGGAGAACGGGAAGGAGACGCTGCAGCGCGCAG
Seq A exon
GTACCAGGGGCAGTGGGGAGCCTTCCCCATCTCCTATAGATCTCCCGGGATGGCCTCCCACGAGGAGGGGAGGAAAATGGGATCAGCACTGGAATATCGCCCTCCCTTGAATGGAGAATGGCATGAGTTTTCCTGAGTTTCCTCTGAGGGCCCCCTCTGCTCTCTAGGACAATTAAGGGATGAAGTCTCTGAGGAAATGGAGGGGAAGACAGTCCCTGGAATACTGATCAGGGGTCTCCTTTGACCACTTTGACCACTGCAGCAGCTGTGGTCAGGCTGCTGACCTTTCTCTCAGGCCTTGTTCTCTGCCTCACACTCAATGTGTCTGAAGGTTTGATTCCAGCTTTTCTGAGTCCTGCAGCCTCCACTCAGGTCAGGACCAGAAGTCGCTGTTCCTCCCTCAGAGACTAGAACTTTCCAATGAATAGGAGATTATCCCAGGTGCCTGTGTCCAGGCTGGCGTCTGGGTTCTCTGCCGCCTTCCCCACCCCAGGTGTCCTGTCCATTCTCAGGATGGTCACATGGGCGCTGCTGGAGTGTCCCAAGAGAGATGCAAAGTGTCTGAATTTTCTGACTCTTCCCGTCAG
Seq C2 exon
AACCCCCAAAGACACACGTGACCCACCACCCCCTCTCTGACCATGAGGCCACCCTGAGGTGCTGGGCCCTGGGCTTCTACCCTGCGGAGATCACACTGACCTGGCAGCGGGATGGGGAGGACCAGACCCAGGACACCGAGCTTGTGGAGACCAGGCCAGCAGGAGATGGAACCTTCCAGAAGTGGGCAGCTGTGGTGGTGCCTTCTGGACAAGAGCAGAGATACACGTGCCATATGCAGCACGAGGGGCTGCAAGAGCCCCTCACCCTGAGCTGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000206435-HLA-C:NM_002117:3
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
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTACATCGCCCTGAACGAGGA
R:
GAAGGTTCCATCTCCTGCTGG
Band lengths:
358-945
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)