MmuINT0140194 @ mm10
Intron Retention
Gene
ENSMUSG00000026927 | Sdccag3
Description
serologically defined colon cancer antigen 3 [Source:MGI Symbol;Acc:MGI:1915362]
Coordinates
chr2:26386904-26387671:-
Coord C1 exon
chr2:26387556-26387671
Coord A exon
chr2:26387312-26387555
Coord C2 exon
chr2:26386904-26387311
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:ENSMUST00000028293:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.415 A=NA C2=0.795
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0026115=Tropomyosin=PU(12.9=17.6),PF131661=AAA_13=PU(16.7=14.7),PF0076914=ERM=PU(10.6=14.0)
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
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types