HsaINT1042979 @ hg38
Intron Retention
Gene
ENSG00000138385 | SSB
Description
Sjogren syndrome antigen B [Source:HGNC Symbol;Acc:HGNC:11316]
Coordinates
chr2:169810858-169811323:+
Coord C1 exon
chr2:169810858-169811044
Coord A exon
chr2:169811045-169811182
Coord C2 exon
chr2:169811183-169811323
Length
138 bp
Sequences
Splice sites
5' ss Seq
AAGGTCATT
5' ss Score
4.32
3' ss Seq
GCTCAATTGTGTCTCTACAGGTC
3' ss Score
10
Exon sequences
Seq C1 exon
GGGATAATTCTATTTAAAGAAAAAGCCAAGGAAGCATTGGGTAAAGCCAAAGATGCAAATAATGGTAACCTACAATTAAGGAACAAAGAAGTGACTTGGGAAGTACTAGAAGGAGAGGTGGAAAAAGAAGCACTGAAGAAAATAATAGAAGACCAACAAGAATCCCTAAACAAATGGAAGTCAAAAG
Seq A exon
GTCATTTATTCTGATTTTTCTTTAACAGTTTGGTTGTTGAACCCATTTACTTGAGCAAAAACTTTAATCAGTGTTCAAAAACATTGACAAGAGACTTAAAAAAAGTTCTTTACAGAGTGCTCAATTGTGTCTCTACAG
Seq C2 exon
GTCGTAGATTTAAAGGAAAAGGAAAGGGTAATAAAGCTGCCCAGCCTGGGTCTGGTAAAGGAAAAGTACAGTTTCAGGGCAAGAAAACGAAATTTGCTAGTGATGATGAACATGATGAACATGATGAAAATGGTGCAACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000138385:ENST00000260956:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.317 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF087776=RRM_3=FE(59.6=100)
A:
NA
C2:
PF087776=RRM_3=PD(1.0=2.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Cow
(bosTau6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAAGCCAAGGAAGCATTGGGT
R:
CGTTTTCTTGCCCTGAAACTGT
Band lengths:
255-393
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains