MmuINT0140194 @ mm9
Intron Retention
Gene
ENSMUSG00000026927 | Sdccag3
Description
serologically defined colon cancer antigen 3 [Source:MGI Symbol;Acc:MGI:1915362]
Coordinates
chr2:26242424-26243191:-
Coord C1 exon
chr2:26243076-26243191
Coord A exon
chr2:26242832-26243075
Coord C2 exon
chr2:26242424-26242831
Length
244 bp
Sequences
Splice sites
5' ss Seq
AAGGTACAT
5' ss Score
7.87
3' ss Seq
TTTCTCTCCACTGTTTTTAGGAA
3' ss Score
10.36
Exon sequences
Seq C1 exon
GTGACAAACTTGAAGACCTTGAAGAAGCCAATCCATTCTCCTTCAAAGAGTTTTTGAAAACCAAGAACCTCAGCCTGTCAAAAGAAGACACGACCACCAGCCGAATTTACCCAAAG
Seq A exon
GTACATCTGGGAAGCTGTCAGTGGTTGCCTTAAAGGACATCTCTTGTACCTTACAGCTTTGGAGGCAGACACTTGAGTGTGGGGAGCAAAGCAGGACAGATATGGCTGCTGACAGAGAGACTGTGTATGGGTGGAACAGCTGCTTGGCCCCCTTTTGGTAGATGAGATGGGCCTTCTTTGTGGGAGCATAGAGAAGGCTGAGCATTGGCTTCCAGTCTGCAGTGTTTCTCTCCACTGTTTTTAG
Seq C2 exon
GAAGCCTCAAGGCACCCACTGGGACTAGAGCACAGCTCCCCTGCCTCCCAGCTCATGGGATATGGCCTGGAATCTCAGCAGCCATTTTTTGAAGACCCAACAAGAGCCAGCAACCTAGAGGAGGATGAAGATGATGGATGGAATATAACCTACTTGCCATCTGCCGTGGATCAGACTCATTCCTCTAGAGACACACAGGACTCACCGCCCTGTGACACCTACCTTTCCTTTTTCTCCAACTCGTCAGAGCTGGCATGTCCCGAGTCTTTGCCCCCATGGACGCTGAGTGACACCGACTCCAGGATCTCCCCAGCGTCTCCAGCTGGGAGTCCTAATGCAGACTTTGCAGCTCATGAAGAATCCCTAGGGGACAGACACCTGCGGACGCTGCAGATAAGTTATGAAGCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026927-Sdccag3:NM_001085408:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.419 A=NA C2=0.794
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0076914=ERM=PU(10.6=14.0),PF0026115=Tropomyosin=PU(12.9=17.6),PF131661=AAA_13=PU(16.7=14.7),PF138631=DUF4200=PU(1.9=1.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACGACCACCAGCCGAATTTAC
R:
CAAAGACTCGGGACATGCCAG
Band lengths:
297-541
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
Other AS DBs: