RnoINT0138591 @ rn6
Intron Retention
Gene
ENSRNOG00000018525 | Slc4a9
Description
solute carrier family 4 member 9 [Source:RGD Symbol;Acc:628811]
Coordinates
chr18:29356191-29356806:+
Coord C1 exon
chr18:29356191-29356324
Coord A exon
chr18:29356325-29356543
Coord C2 exon
chr18:29356544-29356806
Length
219 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGA
5' ss Score
9.79
3' ss Seq
ACTGTCTCTCATTCTCACAGAGA
3' ss Score
10.05
Exon sequences
Seq C1 exon
GGAGTGCTGGAGAGTTTCCTGGGCACAGCGGTGGCTGGAGCCACCTTCTGCCTGATGGCAGGTCAGCCCCTCACTATCCTTAGCAGCACAGGGCCAGTGCTGGTATTTGAGCGCCTACTTTTTTCTTTTAGCAG
Seq A exon
GTAGGAGATCTCTCTCACCTCTGCAGCCCGTTGGGTGGGCGTATCCTCCATTGGTCCTAACTGGGTGAAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGGTAGAGGGGGGGGGACTGTCTCTGGCTTGAGGGGTACTTGATCTGGGTTAGGTAAGGAGGAGACAGCCCTGACTGTCTCTCATTCTCACAG
Seq C2 exon
AGATTACAGCCTGGACTACCTGCCCTTCCGCCTGTGGGTAGGCATCTGGGTGGCCACATTTTGCCTGGCACTGGTGGCTACCGAGGCCAGCTTGCTGGTGCGCTACTTCACCAGATTCACAGAGGAAGGGTTCTGTGCCCTCATCAGCCTCATCTTTATTTATGATGCTGTGGGGAAGATGCTGAACTTGATCCGTGCCTATCCAATCCAAAGGCCAGGATCTCCTGCCTACAGTTGCTTCTGTCAATACCCAGGCACAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000018525:ENSRNOT00000025137:10
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:
PF0095516=HCO3_cotransp=FE(8.6=100)
A:
NA
C2:
PF0095516=HCO3_cotransp=FE(17.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping 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
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGCTGGTATTTGAGCGCCTAC
R:
TCCTGTGCCTGGGTATTGACA
Band lengths:
299-518
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]