HsaEX0040046 @ hg19
Exon Skipping
Gene
ENSG00000153029 | MR1
Description
major histocompatibility complex, class I-related [Source:HGNC Symbol;Acc:4975]
Coordinates
chr1:181019147-181022813:+
Coord C1 exon
chr1:181019147-181019422
Coord A exon
chr1:181021371-181021646
Coord C2 exon
chr1:181022709-181022813
Length
276 bp
Sequences
Splice sites
3' ss Seq
CTTTAGCTTCTTCTTCCTAGAGC
3' ss Score
5.66
5' ss Seq
AGGGTAAGG
5' ss Score
9.16
Exon sequences
Seq C1 exon
GGTCTCACACTTACCAGAGAATGATTGGCTGTGAGCTGCTGGAGGATGGAAGCACCACAGGATTTCTGCAGTATGCATATGACGGGCAGGATTTCCTGATCTTCAATAAAGACACCCTCTCCTGGCTGGCTGTAGATAATGTGGCTCACACCATCAAGCAGGCATGGGAGGCCAATCAGCATGAGTTGCTGTATCAAAAGAATTGGCTGGAAGAAGAATGTATTGCCTGGCTAAAGAGATTCCTGGAGTATGGGAAAGACACCCTACAAAGAACAG
Seq A exon
AGCCCCCACTGGTCAGAGTAAATCGCAAAGAAACTTTTCCAGGGGTTACAGCTCTCTTCTGCAAAGCTCATGGCTTTTACCCCCCAGAAATTTACATGACATGGATGAAAAACGGGGAAGAAATTGTCCAAGAAATTGATTATGGAGACATTCTTCCCAGTGGGGATGGAACCTATCAGGCGTGGGCATCAATTGAGCTTGATCCTCAGAGCAGCAACCTTTACTCCTGTCATGTGGAGCACTGCGGTGTCCACATGGTTCTTCAGGTCCCCCAGG
Seq C2 exon
AATCAGAAACTATCCCTCTTGTGATGAAAGCTGTCTCTGGGTCCATTGTCCTTGTCATTGTGCTGGCTGGAGTTGGTGTTCTAGTCTGGAGAAGAAGGCCCCGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000153029_MULTIEX1-4/5=3-5
Average complexity
S
Mappability confidence:
100%=100=100%
Protein Impact
Alternative protein isoforms (Ref)
Show PDB structure
Features
Disorder rate (Iupred):
C1=0.001 A=0.011 C2=0.000
Domain overlap (PFAM):
C1:
PF0012913=MHC_I=PD(50.0=94.6)
A:
PF064417=EHN=FE(52.9=100),PF0765410=C1-set=WD(100=88.2)
C2:
PF064417=EHN=PD(9.2=44.4)
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATGATTGGCTGTGAGCTGCTG
R:
TGGACCCAGAGACAGCTTTCA
Band lengths:
301-577
Functional annotations
There are 1 annotated functions for this event
PMID: 32963314
This event
The full-length isoform, MR1A, can activate Mucosal Associated Invariant T (MAIT) cells. Using a transcriptomic analysis in conjunction with qPCR, the authors find that that MR1A and MR1B (skipping of HsaEX0040046) transcripts are widely expressed. However only MR1A can present mycobacterial antigen to MAIT cells. Coexpression of MR1B with MR1A decreases MAIT cell activation following bacterial infection. Additionally, expression of MR1B prior to MR1A lowers total MR1A abundance, suggesting competition between MR1A and MR1B for either ligands or chaperones required for folding and/or trafficking. Finally, the authors evaluated CD4/CD8 double positive thymocytes expressing surface MR1. Relative expression of MR1A/MR1B transcript is associated with the prevalence of MR1 + CD4/CD8 cells in the thymus.
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)