HsaEX0030119 @ hg19
Exon Skipping
Gene
ENSG00000204622 | HLA-J
Description
major histocompatibility complex, class I, J (pseudogene) [Source:HGNC Symbol;Acc:4967]
Coordinates
chr6:29976815-29977733:+
Coord C1 exon
chr6:29976815-29976954
Coord A exon
chr6:29977097-29977144
Coord C2 exon
chr6:29977312-29977733
Length
48 bp
Sequences
Splice sites
3' ss Seq
CTGTTTTTGTTCTACCCCAGGCA
3' ss Score
9.83
5' ss Seq
AAGGTGAGA
5' ss Score
8.68
Exon sequences
Seq C1 exon
TCACACATTTCTGGAAACTTCTCAAGGTTCCAAGACTAGGAGGTTCCTCTAGGACCTCATGGCCCTGCTACCTTCCTGGCCTCTCACAGGACGTTTTCTTCCCGCAGATAGAAAAGGAGGGAGCTACTCTCAGGCTGCAA
Seq A exon
GCAGCCAAAGTGCCCAGGGCTCTGATGTGTCTCTCACGGCTTGTAAAG
Seq C2 exon
TGTGAGACAGCTGCCTTGTGTGGGACTGAGAGGCAAGATTTGTTCATGCCTTCCCTTTGTGACTTCAAGAACCCTGACTTCTCTTTCTGCAAAGGCATCTGAATGTGTCTGTGTCCCTATAGGCATAATGTGAGGTGGTGGGGAGACCAGCCCACACCCGTGTCCACCATGACCCTGTTCCCCACACTGACCTACATTCCTTCCCCGATCACCTTTCCTGTTCCAGAGAAGTGGTGCTGGGATGTCTCCATCTCTGTCTCAACTTCATGGTGCACTGAGCTGTAACTTCTTACTTCCCTATTAAAATTAGAATCTGAGTATAAATTTACTTTTTTCAAATTATTTCCATGACGGGTTGATGGGTTAATTAAAGGAGAAGATTCCTAAAATTTGAGAGACAAAATAAATGGAAGACATGAGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000204622_CASSETTE3
Average complexity
S
Mappability confidence:
100%=100=100%
Protein Impact
NonCoding
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
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:
TTCCTCTAGGACCTCATGGCC
R:
ATCTTGCCTCTCAGTCCCACA
Band lengths:
136-184
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- The Cancer Genome Atlas (TCGA)
- Genotype-Tissue Expression Project (GTEx)
- 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)