HsaINT0159323 @ hg19
Intron Retention
Gene
ENSG00000138385 | SSB
Description
Sjogren syndrome antigen B (autoantigen La) [Source:HGNC Symbol;Acc:11316]
Coordinates
chr2:170667368-170667833:+
Coord C1 exon
chr2:170667368-170667554
Coord A exon
chr2:170667555-170667692
Coord C2 exon
chr2:170667693-170667833
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-SSB:NM_003142:10
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.286 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
Rat
(rn6)
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]
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)