GgaINT0046767 @ galGal4
Intron Retention
Gene
ENSGALG00000009677 | SSB
Description
Gallus gallus Sjogren syndrome antigen B (autoantigen La) (SSB), transcript variant 2, mRNA. [Source:RefSeq mRNA;Acc:NM_204580]
Coordinates
chr7:18076540-18077003:-
Coord C1 exon
chr7:18076820-18077003
Coord A exon
chr7:18076663-18076819
Coord C2 exon
chr7:18076540-18076662
Length
157 bp
Sequences
Splice sites
5' ss Seq
AAGGTCCTC
5' ss Score
-0.12
3' ss Seq
CTGTCATCTTATCCCAACAGGAC
3' ss Score
11.42
Exon sequences
Seq C1 exon
GGAATCATCCTATTTAAGGATGCTGCAAAAGAAGCTCTGGAAAAAGCTAAGGAAGCACATAATGGAAACTTACAGCTTCGGAACAAAGATGTTACTTGGGAATTGCTAGAAGGAGATGCAGAGAAAGAAGCTCTGAAAAAAATACTAGAAGATCAGCAGGAATTGCTGAAACAGAAAGGAAAAG
Seq A exon
GTCCTCTCTGACTTGTTGAAGCATTTACAATGTTCTAGGAGTGGTGTTATGTATTCACAATTTTGTTTTCACAAAATCATCACTAACTGTAAAGCATTATTTTCAGCTTGTCAATTAAAAGACATGATACCAAGTTCCTGTCATCTTATCCCAACAG
Seq C2 exon
GACGCAAACTTAAAGGAAGAGGGGGGAAGATGGCTCAAGGTGCACACAAAGGGAAGGTACAGTTTCAGGGCAAGAAAATAAAGTTTGAGAATGAGGAAGGCGGCGAAGATGATACTAAAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009677:ENSGALT00000015751:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.355 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF087776=RRM_3=FE(58.7=100)
A:
NA
C2:
PF087776=RRM_3=PD(1.9=4.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGGATGCTGCAAAAGAAGCTCT
R:
TCTTGCCCTGAAACTGTACCT
Band lengths:
243-400
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]