RnoINT0138605 @ rn6
Intron Retention
Gene
ENSRNOG00000018525 | Slc4a9
Description
solute carrier family 4 member 9 [Source:RGD Symbol;Acc:628811]
Coordinates
chr18:29354432-29354945:+
Coord C1 exon
chr18:29354432-29354589
Coord A exon
chr18:29354590-29354857
Coord C2 exon
chr18:29354858-29354945
Length
268 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
GTCCTCCATTCCTTCCTCAGGTT
3' ss Score
11.04
Exon sequences
Seq C1 exon
CACCAGAACCCCCTGAGACAGAAGCTGCCTCCAGGAGCTGAGGCAGCGGCAGTGTTGGCAGGAGAGCTGGGCTTCCTGGAACAGCCACTAGCGGCCTTTGTAAGACTGCAGAACCCGGTGGTGCTGGAGCCTCTTACAGAGGTGGTCCTGCCTAGCAG
Seq A exon
GTGAGGTGACTGAATCAGGGCTCTGGGACCCAGAAGGGCCTCTACTGAGGAGGGGTGGGGTCTTCGGATATGGTTCCCCAACAGTGTCTAAGAAATGCTCCCCGGAGGTCATTCTGCAGAGCTGGTGTGTCCTTGGGCAAAGCTAAGTGTCAGTCAGAGGCTTCTCATATCAGCAGGCAATGCTGTCCTATGAGAAAGCAACCTGGAGTTGCTTTCCCATTCTGCCCAGATTTCCCTCGAAACCCACAGTCCTCCATTCCTTCCTCAG
Seq C2 exon
GTTTTTCTGCCTCCTCTTGGGTCCTCCCACCCTGGGAAGGAGCTATCATGAGACGGGACGGGCAGCAGCTGTCCTCCTCAGTGACCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000018525:ENSRNOT00000025137:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.113 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF075658=Band_3_cyto=FE(37.1=100)
A:
NA
C2:
PF075658=Band_3_cyto=FE(20.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCAGAACCCCCTGAGACAGAA
R:
AGGGTCACTGAGGAGGACAG
Band lengths:
244-512
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]