RnoINT0138601 @ rn6
Intron Retention
Gene
ENSRNOG00000018525 | Slc4a9
Description
solute carrier family 4 member 9 [Source:RGD Symbol;Acc:628811]
Coordinates
chr18:29353285-29353909:+
Coord C1 exon
chr18:29353285-29353445
Coord A exon
chr18:29353446-29353795
Coord C2 exon
chr18:29353796-29353909
Length
350 bp
Sequences
Splice sites
5' ss Seq
TGGGTAGGA
5' ss Score
5.12
3' ss Seq
ACGTCACATCTGCTCTCCAGAGC
3' ss Score
5.85
Exon sequences
Seq C1 exon
GTGGCTGCTGTTTGAGGAGAAGCTAGACATAGGCGCGGGCCGATGGAGTGCCCCCCATGTGCCTACCTTGGCGCTCCCCAGCCTGCAGAAGCTTCGAGGTCTGTTGGCCGAGGGCATTGTATTGCTAGACTGTCCGGCTCGGAGCCTCCTGGAGCTTGTGG
Seq A exon
GTAGGAAGACATCCCATTTCCTGGGAATTTCTTAGAATCTTTCCTAGCCTATCTCACCCCATCCTACCCCAGGGACTGCCCACTTCTGCCTCAGACAGTGATGGTGGGCAGCTGGGTGCTGTGGCTGGAATTTCAGCACTTGACAGGCGGAGGCAGGAGGACCACTGAAAATTGGGCAGCTCTGTTTATGTAGTAAGACCTTGACTCAAAACAACAGTGTGTGTTGGGGGGAGGGTCACTGACCCTTGTATTTCTGAGGAAAGGCACATGAAAGGAGAGGCAGGAAGGGGAGTCAGTGGGAGGACAGACAGCGCTCAGGAGTGGAGTTGAACGTCACATCTGCTCTCCAG
Seq C2 exon
AGCAGGTCGTCAGTGGCGAGTCGCTGAGCCCAGAACTGAGAGGGCAGCTTCAGGCCTTGCTCCTGCAGAGACCCCAGCACCACATCCAGACCACAGGCATCCGGCCCTGCAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000018525:ENSRNOT00000025137:2
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:
PF075658=Band_3_cyto=PU(52.8=85.5)
A:
NA
C2:
PF075658=Band_3_cyto=FE(42.7=100),PF075658=Band_3_cyto=PU(2.9=10.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGGCTGCTGTTTGAGGAGAA
R:
GATGCCTGTGGTCTGGATGTG
Band lengths:
262-612
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]