RnoINT0137693 @ rn6
Intron Retention
Gene
ENSRNOG00000018649 | Slc35c2
Description
solute carrier family 35 member C2 [Source:RGD Symbol;Acc:1311250]
Coordinates
chr3:161805597-161806210:-
Coord C1 exon
chr3:161806138-161806210
Coord A exon
chr3:161805766-161806137
Coord C2 exon
chr3:161805597-161805765
Length
372 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGC
5' ss Score
8.05
3' ss Seq
CCGCACTGTCCCCCCTCTAGCGT
3' ss Score
7.89
Exon sequences
Seq C1 exon
GTACACAATGACCAAATCCTCTGCTGTGCTCTTTATCCTGATCTTCTCTCTGATCTTCAAGCTGGAGGAGCTG
Seq A exon
GTGAGCCCCACATTGTCACTCTGTGGCAGGACACTGCCGGCCCCATGTCTCTGGAATGTCTTTCTTGGGGAGGGGACCTAGATATGGGTGACAGCTGAAGGTTTAGAAGTAAGCGTGGCAGGGTCAGCGTGGGCCCCGGGCCCTGGGATTCCCCTGGGGCAACTCAGCGGGTCCTGTTTGTTAAGGGGCACTTGGAGCCTGGAAGGGACACCAGTACTTGAGTATTTCAGAACAAGTATGATGTTAGGAACATGCTTGCTGCATGTCAGCCTTGAGTCCGTCAGTAGGCTTTGGAGGGGACGAGGCATAGAAGGAGACACGGCACATGCTTGAGCCTGGAGCTCCCAGTGAGCCGCACTGTCCCCCCTCTAG
Seq C2 exon
CGTGCAGCGCTGGTCCTGGTGGTCCTGCTCATTGCTGGCGGCCTCTTCATGTTTACCTATAAGTCCACGCAGTTCAACGTGGAGGGCTTTGCCTTGGTGCTGGGGGCTTCGTTCATTGGCGGCATCCGCTGGACCCTTACACAAATGCTTCTTCAGAAAGCTGATCTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000018649:ENSRNOT00000025238:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0315111=TPT=PU(18.5=49.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Human
(hg19)
No conservation detected
Mouse
(mm9)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATGACCAAATCCTCTGCTGTGC
R:
TCAGCTTTCTGAAGAAGCATTTGTG
Band lengths:
230-602
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]