RnoINT0138608 @ rn6
Intron Retention
Gene
ENSRNOG00000018525 | Slc4a9
Description
solute carrier family 4 member 9 [Source:RGD Symbol;Acc:628811]
Coordinates
chr18:29355606-29356049:+
Coord C1 exon
chr18:29355606-29355722
Coord A exon
chr18:29355723-29355874
Coord C2 exon
chr18:29355875-29356049
Length
152 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
TGACGACCCGTGGGCGGGAGGCT
3' ss Score
-6.91
Exon sequences
Seq C1 exon
ATTTCCCTCGAAACTGCAGGAGGTCACCAGCCTCTCCCGCCAGAGTGCTGCCTTGGCAGAAAACAAGCACCACCATGGGCCGCACACACCCATCCCAGAATTGCAAAGGACGGGCAG
Seq A exon
GTGAGGGGAGCTTGCTGGGAACAAGGGTTGGGATCCTGTGGGAGAGTCACAGAGGCATCAAAATGTGCGGGCAAGGCGGGAGGATACAGAGGAAATCAGGATGCAGGCATGGGATGCGGAAACATGGATCGCTGACGACCCGTGGGCGGGAG
Seq C2 exon
GCTTTTTGGGGGTCTTGTTCAGGACGTGCGCCGGAAGGCATGCTGGTACCCCAGCGATTTCCTGGATGCCCTACATCCCCAGTGTTTCTCAGCGGTGCTCTACATTTACCTGGCCACAGTCACAAATGCCATCACTTTTGGGGGTCTTCTGGGAGATGCCACCGAAGGTGCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000018525:ENSRNOT00000025137:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.475 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0095516=HCO3_cotransp=PU(1.2=15.0)
A:
NA
C2:
PF0095516=HCO3_cotransp=FE(11.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCGAAACTGCAGGAGGTCAC
R:
GACCCCCAAAAGTGATGGCAT
Band lengths:
257-409
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]