MmuINT0147294 @ mm9
Intron Retention
Gene
ENSMUSG00000024485 | Slc4a9
Description
solute carrier family 4, sodium bicarbonate cotransporter, member 9 [Source:MGI Symbol;Acc:MGI:2443384]
Coordinates
chr18:36690754-36691180:+
Coord C1 exon
chr18:36690754-36690870
Coord A exon
chr18:36690871-36691087
Coord C2 exon
chr18:36691088-36691180
Length
217 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
TGGATGCCCTACACCCCCAGTGT
3' ss Score
4.98
Exon sequences
Seq C1 exon
ATTCCCCTCGAAACTGCAGGAGGTCACCAGCCTCTCCCGACAGAGTGCTGCCCTAGCAGAAGACAAGCACCATCACGGACCGCACACACCCATCCCAGAATTGCAAAGGACAGGCAG
Seq A exon
GTGAGGGCAGCTGGGTGGGAACAAGGGTTGGGATCCTGTGGAAGAGTTACAGAGACATCAAAATGTGCAGGCAGTGCGGGAGGATGCAGGTGTGGGGTGTGGAAACCTGGATCACTGATGACCCACGGGTGGGAGGCTCTTTGGGGGTCTTATTCAGGACGTGCGCCGGAAGGCATGTTGGTACACCAGTGATTTCCTGGATGCCCTACACCCCCAG
Seq C2 exon
TGTTTCTCAGCTGTGTTCTACATTTACCTGGCCACAGTCACAAACGCCATCACTTTTGGGGGTCTTCTGGGAGATGCCACTGAAGGTGCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024485-Slc4a9:NM_172830:8
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.433 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0095516=HCO3_cotransp=PU(1.3=15.0)
A:
NA
C2:
PF0095516=HCO3_cotransp=PU(4.3=56.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATTCCCCTCGAAACTGCAGGA
R:
ACCTTCAGTGGCATCTCCCAG
Band lengths:
204-421
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: