GgaINT0046762 @ 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
chr7:18078628-18078933:-
Coord C1 exon
chr7:18078826-18078933
Coord A exon
chr7:18078729-18078825
Coord C2 exon
chr7:18078628-18078728
Length
97 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGCT
5' ss Score
6.77
3' ss Seq
GAATATATCTTACTCAACAGGGG
3' ss Score
6.63
Exon sequences
Seq C1 exon
AAAGGCTTTCCATTGGATGCAACTCTCGATGATATCAAAGAATGGCTGGAGGATAAAGGTCCTGTTGAAAACATTCAAATGAGGAGAACGCTGCAGAAAACATTTAAG
Seq A exon
GTAGCTATTGCAATGAACAATTAGACCTGGGTCAGGGATGCCTTATGGAGTATATTTTGTTAAATTATTCTAAAATTGAATATATCTTACTCAACAG
Seq C2 exon
GGGTCAATATTTGCGGTTTTTGATAGTGTTGAATCTGCCAAGAAGTTCACAGAAATCCCAAACCAAAAGTACAAAGACACGGAGCTGATAGTGCTTTTCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009677:ENSGALT00000015751:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.028 A=NA C2=0.015
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
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATGGCTGGAGGATAAAGGTCC
R:
TGAAAAGCACTATCAGCTCCGT
Band lengths:
167-264
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]