MmuINT0140199 @ mm9
Intron Retention
Gene
ENSMUSG00000026927 | Sdccag3
Description
serologically defined colon cancer antigen 3 [Source:MGI Symbol;Acc:MGI:1915362]
Coordinates
chr2:26238320-26240341:-
Coord C1 exon
chr2:26240202-26240341
Coord A exon
chr2:26239215-26240201
Coord C2 exon
chr2:26238320-26239214
Length
987 bp
Sequences
Splice sites
5' ss Seq
AAAGTGAGT
5' ss Score
8.4
3' ss Seq
CTGGTCTCTCTCTGCTTTAGGCA
3' ss Score
10.7
Exon sequences
Seq C1 exon
GCCCAGCTCTCAAACTTGAGGCGAGAAAATGAAGCCCTGCGGTCAGGCCAGGGTGCCAGCCTTTCTGTAGTGAAGCAGAACACCGACGTGGCCTTGCAGAACCTCCACCTTGTCATGAACAGTGCACACGCATCCATAAA
Seq A exon
GTGAGTCCCCGGGCGGCCTCTGGCTGGACCAGCAAGGGAAAGGTGCTGACCGGCTCAGTCATACTATAGTCAATCAAGTAAGAGTGGTCTCTTGTTTTGAGACAGGGTCTCACTCTGTAGCACTGACTGGCCTGGAGCTATGTACACTAGGCTGACCTTGACCTCACACAGATCCTTCTGCCTCTGCACTCAAGTGCTAGAGTTCAAAGCATGCACCCCCTCACCTGGCTTGGTTTTTTTTTGAGGGATTTTTGTTTTGTTTGGGTTTTTAAGACAAAGTCTCCCTGGCTTCTCTGACAGTATGTGTAGACCGGGTTAGCCTCAGACTCAGAGATTTCCTGCTTCCATTTCCCAAGTTCTGGAACTTGAGGTATGCATTATCATGCCCGTTTTAGGATTTTTATTTTTGATGTTCCAGAGAACCTTCCCACTAATAGGTGTGGATGATGCCATGCCTCTGAATCCAGCTGCTTTGCCTGTGTACGTTGCAGCTCTAACTGAAGGGGAGAAGTCTGCCACAGTGAGCATACTGTGAGCTAGTCAGTTGGTGATGATAATGGTGATTAAACACTCACCAAAGCTGCAGCTTGTTAAACTTGTCAAGATGTAGTTAATTCATCTGACCTATTAAACACAAAAGCAAAGTAGTCCCCCTGGTAGAGCTCTCATGACTAGATATGGGACTTGCGGTGGGACTACTGCCCACATCACTGAGAGTACTGCATCATCAGCTTGGCCTAAGCAAAGAGCAAAATTCAGAATCAGTTTCTGATGAACTTATCTGGCTTGCAACCTACCATCTTTAGTTGCCTTCCCTAAGCTTCACTATAGGGTGGCTGGCCTGTGCACAGGCACATGGGCCAGAGGGCAGCCACACAGAATCCAGTGTGGCAAACCTGGTTGATAGCTCTGGGCTCTCTCCTTTAGATCTGTCTCTGGCTGCCTTTGCACGGCTGAAATAATGGCCCTGGTCTCTCTCTGCTTTAG
Seq C2 exon
GCAGCTGGTGTCTGGGGCAGACACACTGAACCTTGTTGCTGAAATCCTCAAGTCTATCGACAGAATTAGTGAAGTTAAAGATGAGGTGGACTCTTGAGACGCTCTACCTGCCACCGGGTCCCGTCACCTCTGCACCGAAGGCACCACACATCTTCCGAATGTGTTCCTGTCTATGCAGTCCTCATCAAAGCATTTCACGGCCTAATCATGTGACTGGCCATCTGCAGTACGGGGCTCCTTTCCACCAGTTGAACCTAACAGTTTACATGAAGTCCCACTGTTCGATAGACTCACTGATTTACTGGAAGACACTTTTATAAAACCACTAAAGCTGAAACGACAGTTTTGTAACAAGCTTCTTTCACCACCCTCTCTAGGACGAGGTCGGGCTCAGCCTCAGTGTTGTCAAGTGGAACACGAAGTGAGCCAGTGTGTAAGTGAGCAGCCTGTACAGAGACGCGTGCCTCACTGAGGCAGCACCGCTTGGTACGTGCTGCCGTCCTCCCACCAGGACCATAGGACCAAGGTCACACACTGTGCACAGTGCAAAGCTTCATACACCCTCTACTGTGTGCTGTCAGCTTTGGAAAGCCATTTGGGGCTGTCGATTTTGATGCACGTTAATGTGTTTGTGTGCCTTTTGTATAGTGCAATTCAGACTGGAATTAAAGCACACACCCACCTGGGGGGTCAGCACCAGCTCTTTGGGCTGGCTGGCTGGTTTTTGAAGGACAGGCAAGACATAAGCAGCTCCCTGTGCTGTGCTGAGGGGTCAAGGTTTGGGGGCCACTTTCCTATAGGTTGTTTTTTTGTTTTTTTTTTTTAATTTATTTTCCCTTTTCCCCTCCTGTTGAGATCAACAGCTTTCTGATCTAAATAAATCTTAAAGATCATT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026927-Sdccag3:NM_001085408:7
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.085 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0076914=ERM=FE(25.6=100),PF0026115=Tropomyosin=FE(24.7=100),PF131661=AAA_13=PD(12.5=31.9),PF138631=DUF4200=PD(15.5=34.0),PF052669=DUF724=PD(19.0=40.4)
A:
NA
C2:
PF0076914=ERM=PD(16.7=90.9),PF0026115=Tropomyosin=PD(16.7=93.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGGCGAGAAAATGAAGCCCTG
R:
GTACTGCAGATGGCCAGTCAC
Band lengths:
352-1339
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: