GgaINT0125718 @ galGal4
Intron Retention
Gene
ENSGALG00000001921 | SDCCAG3
Description
serologically defined colon cancer antigen 3 [Source:HGNC Symbol;Acc:HGNC:10667]
Coordinates
chr17:7891188-7891499:+
Coord C1 exon
chr17:7891188-7891250
Coord A exon
chr17:7891251-7891359
Coord C2 exon
chr17:7891360-7891499
Length
109 bp
Sequences
Splice sites
5' ss Seq
CAGGTACAA
5' ss Score
7.09
3' ss Seq
GGCTTTATTTCCCTCCCAAGGTT
3' ss Score
8.18
Exon sequences
Seq C1 exon
AAACGGGCTGTTAAGGCAGAAAATAATGCTACGAAACTGAAACAGGAAAATGCATTACTTCAG
Seq A exon
GTACAAAGCAGTGCCGTTCTCAAGGCCTCCTGCTGCTGCTGCTGCACCTCGCTCAGTGCTGCGAGTTCTGTGTTGTTCTCATTACCGAGGGCTTTATTTCCCTCCCAAG
Seq C2 exon
GTTCAGCTGAAGAATTACAAGATGGAGAACGAAGCTCTGAGGTCGGGGCAGTCAGCAAGCCTGGCTGCGGTGAAACAGAACGCAGACACGGCCCTACAGAACCTCCTGACTGTTATCACAAACTCTCAGTCTTCGATAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000001921:ENSGALT00000002974:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.262 A=NA C2=0.064
Domain overlap (PFAM):
C1:
PF154191=LNP1=FE(12.6=100),PF0076914=ERM=FE(11.6=100)
A:
NA
C2:
PF154191=LNP1=PD(17.6=59.6),PF0076914=ERM=FE(26.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTGTTAAGGCAGAAAATAATGCT
R:
ATCGAAGACTGAGAGTTTGTGA
Band lengths:
194-303
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]