HsaINT1015600 @ hg38
Intron Retention
Gene
ENSG00000204632 | HLA-G
Description
major histocompatibility complex, class I, G [Source:HGNC Symbol;Acc:HGNC:4964]
Coordinates
chr6:29829418-29829932:+
Coord C1 exon
chr6:29829418-29829693
Coord A exon
chr6:29829694-29829815
Coord C2 exon
chr6:29829816-29829932
Length
122 bp
Sequences
Splice sites
5' ss Seq
GGAGTAAGG
5' ss Score
4.33
3' ss Seq
ACCTTCACCTCCTTTCCCAGAGC
3' ss Score
9.41
Exon sequences
Seq C1 exon
ACCCCCCCAAGACACACGTGACCCACCACCCTGTCTTTGACTATGAGGCCACCCTGAGGTGCTGGGCCCTGGGCTTCTACCCTGCGGAGATCATACTGACCTGGCAGCGGGATGGGGAGGACCAGACCCAGGACGTGGAGCTCGTGGAGACCAGGCCTGCAGGGGATGGAACCTTCCAGAAGTGGGCAGCTGTGGTGGTGCCTTCTGGAGAGGAGCAGAGATACACGTGCCATGTGCAGCATGAGGGGCTGCCGGAGCCCCTCATGCTGAGATGGA
Seq A exon
GTAAGGAGGGAGATGGAGGCATCATGTCTGTTAGGGAAAGCAGGAGCCTCTCTGAAGACCTTTAACAGGGTCGGTGGTGAGGGCTGGGGGTCAGAGACCCTCACCTTCACCTCCTTTCCCAG
Seq C2 exon
AGCAGTCTTCCCTGCCCACCATCCCCATCATGGGTATCGTTGCTGGCCTGGTTGTCCTTGCAGCTGTAGTCACTGGAGCTGCGGTCGCTGCTGTGCTGTGGAGAAAGAAGAGCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000204632:ENST00000360323:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.194 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0012913=MHC_I=PD(8.1=8.6),PF0765410=C1-set=WD(100=91.4)
A:
NA
C2:
PF0012913=MHC_I=PD(8.1=20.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Cow
(bosTau6)
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:
GATCATACTGACCTGGCAGCG
R:
ACTACAGCTGCAAGGACAACC
Band lengths:
258-380
Functional annotations
There are 1 annotated functions for this event
PMID: 7989753
This event
Generates a soluble form. The open reading frame in this mRNA continues into intron 4 terminating 21 amino acids after the alpha 3 domain, thus excluding the transmembrane encoding region and yielding a protein with a highly charged carboxyl terminus. Transfection of the intron 4 containing cDNA, inserted into a retroviral expression vector, into LCL .221 followed by comparison of the class I protein to native soluble G by two dimensional isoelectric focusing/SDS-PAGE analysis, demonstrated this message encoded the soluble HLA-G protein. In addition, a similar intron containing message derived from the HLA-G2 mRNA was found, suggesting the existence of a soluble form of this alternative HLA-G protein.
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains