RnoINT0132060 @ rn6
Intron Retention
Gene
ENSRNOG00000018876 | Sdccag3
Description
serologically defined colon cancer antigen 3 [Source:RGD Symbol;Acc:1305930]
Coordinates
chr3:3827498-3829746:-
Coord C1 exon
chr3:3829607-3829746
Coord A exon
chr3:3828472-3829606
Coord C2 exon
chr3:3827498-3828471
Length
1135 bp
Sequences
Splice sites
5' ss Seq
AAAGTGAGT
5' ss Score
8.4
3' ss Seq
CTGGTGTCTCTCTGTTTTAGGCA
3' ss Score
12.44
Exon sequences
Seq C1 exon
GCACAGCTCTCCAACTTCAAGCGAGAAAACGAAGCCCTTCGGTCAGGCCAGGGTGCCAGCCTTACCGTGGTGAAGCAGAACACCGATGTGGCCTTGCAGAACCTCCATGTTGTCATGAACAGTGCACACGCATCTATAAA
Seq A exon
GTGAGTCCCTGGGGGGCTGGGGATTTAGCTCAGTGGTAGAGCGCTTACCTAGGAAGCGCAAGGCCCTGGGTTCGGTCCCCAGCTCCGAAAAAAAGAACCAAAAAAAAAAAAAAGTGAGTCCCTGGATGGCCTGGCTCTCGGGTGTTCCAGCTCTACAGTCTGACTAGACCAAGAAGGGAAATGTGCTAACCGGCCAGGTCAGCTAGGAAGTCAAGCACGTGGTCTCACTTCATAGCACTGACTGGCCTAGAACCATATATGTAGATTAGGTTGACCTTGAACTCACACGGGTCCTTCTGCCTCTACACTGGAGTGCTAGAATTTAAAGGCATGCGTCACCTCACCTGGCTTGTTTTTTTTGTTTTTGTTTGAGACAAAGTCTCCTGGTGTAGCCCTGGTGGCTCTGGCACTGTGTGTAGAGCAGGCTAGCCTCAGACTCATAGATTTCCTCTTCTATTTCCCATGTCCTGGAACTGAAGGTATGCACTATCATACCATTTTAGGGTTTTTATTTTTAATCTGTTCCAGAGAACCTTCCCACTAATAGATGGCGAATGATGCCAGGACTCTGAATCCAGCTCCTTTACCTGTAGATGCTGCAGCTCTAACTAAAGGGCATGATGTGACTTCCACAGTGAGCATACTGTGTGCTAGTTGTAACTTCCACAGTGAGCAAACTGTGTTCTAGTTGTTGATAATGGCAGTTAAACACTCACTGGAGCTGCAGCTGGTAAAGGTGTTGAGATGTACCTGATTCATCCAACCCCTCTGAGGAGAAAGCACAGTAGTCCTCCTGCCAGCTCTCCTCATGACTCGAGGTGTGGCCTGCAGTGACTGCCGCCCACATCACTGAGTACTGCACCATCAGCTTGGCCTAAGCAAAGAGCAAACTCAGAATCAGTTGCTGATGAACTTGTCTGGCTTCCAGCCCACCTTCTTTGGTTGCCTTCCCTGAGCTTTGCTAGAGGGTGGCTGGCCAGTACACAGCACATGGGCCTGAGGACAGTCACACATAGTCCAGTGTGGCAAACCATGGTTGATCTGAGGAGTTTTCCCTCTAGCTTCTCTCCTTTAGGTCTGTCTCTGGCTGCTTTTGCACAGCTGGAATAATGGCCCTGGTGTCTCTCTGTTTTAG
Seq C2 exon
GCAGCTGGTGTCTGGAGCAGAGACACTGAACCTTGTTGCTGAAATCCTCAAGTCTATCGACAGAATTACTGAAGTTAAGGATGAGGCAGACTCTTGAGAACACGACCTGCCGCCGGGTCCCGGCACCTCTGCACCGATGGCACCACACAGCTTCCAACTGTGCTCCTAACTAAGCAGTCCTCACCAAACCATCTCACAGCCTAAGCACGTGACCGGGCACCTGCAGTACAGGGCTCCTTTCCACCGGTTGCACCTAACAGTTTACATGAAGTCCTTTGGGGAAGTCCCACTGTTTGATAGACTCACTGATTTACTGGAAGACATTTTTATAAAACCCAGCAATTTTTAGAAAGCACTAAAGCTGAAACAACAGTTTGGTAAAAAGCTGCTTCCACTGTCCCTCAGATTTACTATAGGATGAGCTCGGGCTCAGGGCCAGTTTTACTAAGCAGAACACTAAGTGAGCCAGTGTGGAAGCGAGCAGCCTGTACAGGACTCTTGCTGTCACTCTGCCTCACGAACAGACGTTGACATTGTGGCCTTCACGGACGGCTCCTGCTGTCAGCAGCCTCACCGAGGCAGCACCACTCGGTAGATGCTGCTGTCCTACCAGGACCCTAGTACCAAAGTCACAGACTGCATTGCAGAGCGTCACACACGCACTACTCTGGGCTACCAGCTTCGGGAAGCCATTTGAGGCTGTTGGTTTTGATGAGTGTTAATGTGTCAGTGCATCTTTTGCATAGTGCGGTTCAGACTGGAATTAGAGCACACACCTACCTGCCTCAGGTCAGCACCAGTTCTTTGGGCTGGCTGGCTGGTTTTGAAGGACAAGCAGACAAAAGCAGCACCCTGTGCTGTGCTGAGGGGTCAGGGTTTGGGGACCACTTTCCTATAGATTTTTTAAATTTCCCTCTTCCCCTCCTGTTGAGATCAACAGCTTTCTTATCTAAATAAATCTTGAAGATCATTTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000018876:ENSRNOT00000061669:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.085 A=NA C2=0.062
Domain overlap (PFAM):
C1:
PF057016=WEMBL=FE(24.7=100),PF0076914=ERM=FE(25.6=100),PF131661=AAA_13=FE(29.3=100),PF0026115=Tropomyosin=PD(17.1=44.7)
A:
NA
C2:
PF057016=WEMBL=PD(16.7=93.9),PF0076914=ERM=PD(16.7=90.9),PF131661=AAA_13=PD(5.1=24.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACAGCTCTCCAACTTCAAGCG
R:
CGTGCTTAGGCTGTGAGATGG
Band lengths:
347-1482
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]