GgaINT0125717 @ galGal4
Intron Retention
Gene
ENSGALG00000001921 | SDCCAG3
Description
serologically defined colon cancer antigen 3 [Source:HGNC Symbol;Acc:HGNC:10667]
Coordinates
chr17:7890951-7891250:+
Coord C1 exon
chr17:7890951-7891062
Coord A exon
chr17:7891063-7891187
Coord C2 exon
chr17:7891188-7891250
Length
125 bp
Sequences
Splice sites
5' ss Seq
ACTGTAAGT
5' ss Score
8.59
3' ss Seq
CATCCTTTGTTCTCTTTCAGAAA
3' ss Score
12.24
Exon sequences
Seq C1 exon
GATGAAAAAGCTCGAAAGAAAGCTCGAGGAAAACAAAATCAAAGAAGAGAAGGAAGCTCGGGACTTGGAAGCAATGGTGCAGCACGTGGAGCAGAATCTCCAGCTGATGACT
Seq A exon
GTAAGTGCTGCCATCCCCATCTCGTACAGCATTCAGAGCAGAGGTGCTACAACACAAACCACATCGCTTCCCGTGATACCAGCGAGCCTTCCTGCATCTCACGCTCATCCTTTGTTCTCTTTCAG
Seq C2 exon
AAACGGGCTGTTAAGGCAGAAAATAATGCTACGAAACTGAAACAGGAAAATGCATTACTTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000001921:ENSGALT00000002974:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.697 A=NA C2=0.262
Domain overlap (PFAM):
C1:
PF154191=LNP1=FE(23.3=100),PF0076914=ERM=FE(21.5=100)
A:
NA
C2:
PF154191=LNP1=FE(12.6=100),PF0076914=ERM=FE(11.6=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:
AAAAGCTCGAAAGAAAGCTCGA
R:
CTGAAGTAATGCATTTTCCTGTTTCA
Band lengths:
170-295
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]