BtaINT0141251 @ bosTau6
Intron Retention
Gene
ENSBTAG00000008716 | SSB
Description
Bos taurus Sjogren syndrome antigen B (autoantigen La) (SSB), mRNA. [Source:RefSeq mRNA;Acc:NM_176665]
Coordinates
chr2:26596728-26597020:-
Coord C1 exon
chr2:26596913-26597020
Coord A exon
chr2:26596829-26596912
Coord C2 exon
chr2:26596728-26596828
Length
84 bp
Sequences
Splice sites
5' ss Seq
AAGGTATGC
5' ss Score
9.55
3' ss Seq
TTTTCTTCCTTTTTTCAAAGGGT
3' ss Score
9.7
Exon sequences
Seq C1 exon
AAAGGCTTCCCGACAGATGCAGCTCTTGATGACATAAAAGAATGGTTAGAAGATAAAGGTCAAGTACTAAATATTCAGATGAGAAGAACCTTGCACAAAGCATTTAAG
Seq A exon
GTATGCTTGTATGTTGTTACTTTTTCTGGTTGAAAAAAACTGGGATGTAACTTTAAAAAATTCTTTTTCTTCCTTTTTTCAAAG
Seq C2 exon
GGTTCAATATTTGCTGTATTTGATAGTATTGAATCAGCTAAAAAGTTTGTTGAGACCCCTGGCCAGAAGTACAAAGACACAGACCTGTTAATACTTTTCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000008716:ENSBTAT00000011484:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
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
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCGACAGATGCAGCTCTTGAT
R:
TTTGTACTTCTGGCCAGGGGT
Band lengths:
174-258
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]