GgaINT0125715 @ galGal4
Intron Retention
Gene
ENSGALG00000001921 | SDCCAG3
Description
serologically defined colon cancer antigen 3 [Source:HGNC Symbol;Acc:HGNC:10667]
Coordinates
chr17:7889812-7890335:+
Coord C1 exon
chr17:7889812-7890169
Coord A exon
chr17:7890170-7890261
Coord C2 exon
chr17:7890262-7890335
Length
92 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGC
5' ss Score
8.7
3' ss Seq
TGGTTTCTCTTCTCCTGTAGCTG
3' ss Score
9.75
Exon sequences
Seq C1 exon
TATGGCGGCGGCGGAGCTGCCTGAGTCCCCCACCGCCGAGCCCAACCCCTTCTCCTTCCGCGAGTTCGTGCGGAGCAAAGCCCGGAGCGGCGACGGAGCTCCGTCCGTCCGCGCCGAGGAGCCCGTCTTCCTCAGTCCCCGCCCCCCTTCCCCTCCCCAGGCGGCTCAGCTCTGCCCCCTCCTCGGCTCCCCGCTGCTGCCGGGCCCGGCGCCTCCCGGTGGGGCGGAGGAGGACGAAGACGAGGCGGAGTGGAGCGGCAGTTACCGACCCGCGGCCGCTGAACGGGCGCACCTCACTGCGGCCTTCTGTGAGGCCGGGGGGGCGGGCGCTGCTCCGCGGCGGCGCAGCTACGAGGAG
Seq A exon
GTGAGCGGCGCCCCGACAGCCCCGGCGCGATGGGTGCGGGGCCGGACCGCCCCGCTCATCTCTAACGAGGATTGGTTTCTCTTCTCCTGTAG
Seq C2 exon
CTGAAAGCAGAGAACGCCGCGTTGCGGAGGAGGATCCGCGAGCTGCAGGAGATCTCTGGGGCTCAAACAGACGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000001921:ENSGALT00000002974:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.882 A=NA C2=0.560
Domain overlap (PFAM):
C1:
PF154191=LNP1=PU(28.9=38.7),PF0076914=ERM=PU(7.0=10.1)
A:
NA
C2:
PF154191=LNP1=FE(15.1=100),PF0076914=ERM=FE(14.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Mouse
(mm9)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGTGGAGCGGCAGTTACC
R:
TTGAGCCCCAGAGATCTCCTG
Band lengths:
177-269
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]