GgaINT0125716 @ galGal4
Intron Retention
Gene
ENSGALG00000001921 | SDCCAG3
Description
serologically defined colon cancer antigen 3 [Source:HGNC Symbol;Acc:HGNC:10667]
Coordinates
chr17:7890262-7891062:+
Coord C1 exon
chr17:7890262-7890335
Coord A exon
chr17:7890336-7890950
Coord C2 exon
chr17:7890951-7891062
Length
615 bp
Sequences
Splice sites
5' ss Seq
CGTGTGAGT
5' ss Score
7.42
3' ss Seq
TTTTTTTACCTTATTTTAAGGAT
3' ss Score
9.23
Exon sequences
Seq C1 exon
CTGAAAGCAGAGAACGCCGCGTTGCGGAGGAGGATCCGCGAGCTGCAGGAGATCTCTGGGGCTCAAACAGACGT
Seq A exon
GTGAGTGAGGCACGGCGTGGGGGGGGGGAGGTGAAAAGGAGTGGTGTTTGGGAGCTCCCCGGAAAGAGTGCAAAGCGTGGAAGAAGTGAGCCGAACTCTCTCCTGTCTGTTAAAAAGCTTTATCAGATCTGCTTTTTCTTATTGGAAAAGGCTTGGTAAGTGCCCAGTGAGGTGATGCCTTGTGAGTGTATTGAGGCCTCATGCAGCTGAAGTTGTGAGGGTAATGGCAAGGCTCCACAGGAGGCAGTTAACTTTGGTGGGTGATTAACTTGACTTTGGGAGGCATTGAATTCCTGAGGCTCACCAACCCAGTGACTGATCCATGGTAGCGATTTCTCTTTGCTGCTCCCGTGGCGGTGGGTGACTGTTTCAGAACGCTCCAGACTGACTGAACAGACACGCTTTCTGTACAGTTGTGCTGTGTTTAGCTGTTCCCATTAGGGCTAATGGATGACGAATGCAGAAAGCCCTGGAGCTGCAGCCTACAAAGGCCGTTCTGTGAGATGCCTTAATTTTTTATTCCATGAAAGGATAGAGTTTCTCAGTTCTTCTCCTGGAGTCTTCTTGTGGTTATTTTACCAAGAAAAGTACTATTTTTTTTTACCTTATTTTAAG
Seq C2 exon
GATGAAAAAGCTCGAAAGAAAGCTCGAGGAAAACAAAATCAAAGAAGAGAAGGAAGCTCGGGACTTGGAAGCAATGGTGCAGCACGTGGAGCAGAATCTCCAGCTGATGACT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000001921:ENSGALT00000002974:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.560 A=NA C2=0.697
Domain overlap (PFAM):
C1:
PF154191=LNP1=FE(15.1=100),PF0076914=ERM=FE(14.0=100)
A:
NA
C2:
PF154191=LNP1=FE(23.3=100),PF0076914=ERM=FE(21.5=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:
CTGAAAGCAGAGAACGCCGC
R:
GTCATCAGCTGGAGATTCTGCT
Band lengths:
185-800
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]