HsaINT0159328 @ hg19
Intron Retention
Gene
ENSG00000138385 | SSB
Description
Sjogren syndrome antigen B (autoantigen La) [Source:HGNC Symbol;Acc:11316]
Coordinates
chr2:170663295-170663581:+
Coord C1 exon
chr2:170663295-170663402
Coord A exon
chr2:170663403-170663480
Coord C2 exon
chr2:170663481-170663581
Length
78 bp
Sequences
Splice sites
5' ss Seq
AAGGTATGA
5' ss Score
9.11
3' ss Seq
ATTTTCCTTCCTTTTTACAGGGA
3' ss Score
11.13
Exon sequences
Seq C1 exon
AAAGGCTTCCCAACTGATGCAACTCTTGATGACATAAAAGAATGGTTAGAAGATAAAGGTCAAGTACTAAATATTCAGATGAGAAGAACATTGCATAAAGCATTTAAG
Seq A exon
GTATGATAATACAGACTTTTTCTAGTTTTAAAATATATGGGACATAACTTAAAAAAATATTTTCCTTCCTTTTTACAG
Seq C2 exon
GGATCAATTTTTGTTGTGTTTGATAGCATTGAATCTGCTAAGAAATTTGTAGAGACCCCTGGCCAGAAGTACAAAGAAACAGACCTGCTAATACTTTTCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000138385-SSB:NM_003142:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=FE(50.7=100)
A:
NA
C2:
PF0007617=RRM_1=PD(42.0=85.3)
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:
GGCTTCCCAACTGATGCAACT
R:
TGGCCAGGGGTCTCTACAAAT
Band lengths:
170-248
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)