RnoINT0137696 @ rn6
Intron Retention
Gene
ENSRNOG00000018649 | Slc35c2
Description
solute carrier family 35 member C2 [Source:RGD Symbol;Acc:1311250]
Coordinates
chr3:161802063-161803071:-
Coord C1 exon
chr3:161802896-161803071
Coord A exon
chr3:161802193-161802895
Coord C2 exon
chr3:161802063-161802192
Length
703 bp
Sequences
Splice sites
5' ss Seq
AAGGTACAC
5' ss Score
7.56
3' ss Seq
TGTCCTGCCTCTACCCACAGGAA
3' ss Score
12.53
Exon sequences
Seq C1 exon
GTCTCCATTTGTCCACCTCTGAGAAGATCTTCCGCTTCCAGGACCCGGGCCTGCTCCTGTGGGTTCTGGGGAGCCTCCTCCTCGGAGGGATTCTGGCCTTTGGCTTGGGCTTCTCTGAGTTCCTCTTGGTCTCCAGAACCTCGAGCCTCACACTCTCCATTGCTGGCATTTTTAAG
Seq A exon
GTACACACTGGGAGTGACCCCAGACCTACCCGGGCTGGAACCCCGTGAGGGCTTCTAGCAGCTCTGCTCCTGTCTCCGCGCCCTGAGAAGGTTGGAGGACAGACAGCAGAGTGTGATGTGCTGTTATTTCCCCCTGTGGAGCTGAGCAAGTGTCACTTCTCGCCAGTGCACAGCTCTGAGGCTGCAGGCCAAGCCTCACACCACTAGGCCTCCAGTGTGCCCACATTGTACCTGACTGGCAGCTCGAGTTAATGGCAGTGACCTGGGACACTGAATGTTGACCCTTGAAAAGTCCCAGCATTGAGAGCTGGACACTGGTCAGGTCTATGAAGGAGTTTCCATCTAGCCAGGTAGGGCATTGACCCCCAAAGCCAACGTTTGGGTGTTAAGCATCTAGCTATGACGAGGAGAGGCCCATCTCAACAAAGCCACGCTGAGGGCTGTCCATCTGTGGACGCCAAGCAACAGCAGACTCCCTTACCGCGGGGGGCACCTGTGCGGTGGTTTGGGGGTTGGTTGGCATTCTGCTTTTGCTGAGAGTTACACATCTGCACTTCAGTAACACCAGGCCTGCAGGCCAGTGGCCTGGGCACAGAGGCTGCCTGTCATATCAGCTGGTCTGGCTTTGGCCTCAGTGTACACAGAGCCCCACCCTCCAGGCCACAGAGTCAGCCTCTGACCCATGTCCTGCCTCTACCCACAG
Seq C2 exon
GAAGTCTGCACCCTGCTATTGGCAGCTCACCTGCTGGGTGACCAGATCAGCCTTCTGAACTGGCTGGGCTTCGCCCTCTGCCTCTCTGGCATCTCCCTTCACGTGGCCCTCAAGGCCCTACATTCCAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000018649:ENSRNOT00000025238:9
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:
PF0315111=TPT=FE(38.4=100)
A:
NA
C2:
PF0315111=TPT=PD(23.2=79.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Human
(hg19)
No conservation detected
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCTCCATTTGTCCACCTCTGAGA
R:
TGGAATGTAGGGCCTTGAGGG
Band lengths:
302-1005
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]