GgaINT0125719 @ galGal4
Intron Retention
Gene
ENSGALG00000001921 | SDCCAG3
Description
serologically defined colon cancer antigen 3 [Source:HGNC Symbol;Acc:HGNC:10667]
Coordinates
chr17:7891360-7892185:+
Coord C1 exon
chr17:7891360-7891499
Coord A exon
chr17:7891500-7891729
Coord C2 exon
chr17:7891730-7892185
Length
230 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGT
5' ss Score
9.72
3' ss Seq
GCTGTGTTTCTCTCACCCAGGCA
3' ss Score
8.91
Exon sequences
Seq C1 exon
GTTCAGCTGAAGAATTACAAGATGGAGAACGAAGCTCTGAGGTCGGGGCAGTCAGCAAGCCTGGCTGCGGTGAAACAGAACGCAGACACGGCCCTACAGAACCTCCTGACTGTTATCACAAACTCTCAGTCTTCGATAAA
Seq A exon
GTAAGTTGCTTCCAAACACTCTGCTGGCACCACCTCAGGTGCTAAATGTGATAGCAGCAAAAGCCTAAACATCCCCAATAGGTTTTCTTTTTGGGCCGAAACTTGGGTCCTTTGTTATGCCCTGCAGGTCAGTCCCCGTTCTCACTTAGTTGCAATGTGTTTTCATCCGGAAAGCAGTGCCTGTGTGTGCTTTATCCTCTCCAGCCTCACGCTGTGTTTCTCTCACCCAG
Seq C2 exon
GCAGCTGCTCTCTGGAGCAGAATCACTGCAGCTCGTCGCCGATCTCCTGAAATCCATAGACAGAATTTCTGAGGTGTCGGAAGATGGACGGTGAAACCAAACGGATGGGCAGAGCTCCGTACTGAGCGCCGCGGGTGCTGCTGCAGGAGCAGCTGTTCCATCCCTGCAGGTGGCCGAGGATGGAGCCGGCAAAGGGCGGCGCTCAGCCGACAGCGAGCGGGACCGCAGCGCCCTGCTCGGCTCCGGAGACTACTAGCAGGGCTGGCAGGAACGCCCGGCCTCTCCCCTCTCCCCGCTCCCCCAGCGGCCGGAGCTGCGGGAATGGGCGGCCGTGCAGCACGGAGGAGCGGACCCGCTGGGGTTCGGGAAGCGGTGCGGCCGTAGGACCGGGCGCTGCTATCCGCGTAACGGAGCGATTAAAGGCGGACGCGACGCGCGGGTCGCGCTCCTGGCGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000001921:ENSGALT00000002974:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.064 A=NA C2=0.111
Domain overlap (PFAM):
C1:
PF154191=LNP1=PD(17.6=59.6),PF0076914=ERM=FE(26.7=100)
A:
NA
C2:
PF0076914=ERM=PD(16.9=90.6)
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:
GCCCTACAGAACCTCCTGACT
R:
CTAGTAGTCTCCGGAGCCGAG
Band lengths:
306-536
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]