MmuINT0147284 @ mm10
Intron Retention
Gene
ENSMUSG00000024485 | Slc4a9
Description
solute carrier family 4, sodium bicarbonate cotransporter, member 9 [Source:MGI Symbol;Acc:MGI:2443384]
Coordinates
chr18:36539310-36539777:+
Coord C1 exon
chr18:36539310-36539378
Coord A exon
chr18:36539379-36539603
Coord C2 exon
chr18:36539604-36539777
Length
225 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
TTTTCCCCTCATTCTCTCAGTTC
3' ss Score
8.54
Exon sequences
Seq C1 exon
TTCATCCCGATGCCCGTGCTCTACGGCATCTTCCTGTACATGGGGGTAGCCGCGCTCAGCAGCATCCAG
Seq A exon
GTGAGCGCACCACCATCAGCTAGCAAGCCCAGTCCTCATTCCCACACTTGCCAGCCCCTGTCATATCCGTTACCCTGCTTCTCCTGGCCATAGAAACTATGCTGCCATGTTCTAGATGGGGAGGCCAAGGGAACTGTCTTCCCTCCCCGCTGCGGTTCCTATAACTAACCGTGACACCCTCCAAATTGCCCCAACAGCCTGTTTCTTTTCCCCTCATTCTCTCAG
Seq C2 exon
TTCGTGAAGAGAGTGCAGCTATTGTTGATGCCAAGGAAACATCAGCCAGACATGCTGCTCCTGCGGCATGTGCCTCTGAGCAGAGTTCACCTCTTCACAGCCATCCAGCTTGCCTGCCTAGGTCTGCTTTGGGTAGTCAAGTCTACCCCTGCAGCCATTGTCTTCCCACTCATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024485:ENSMUST00000074298:17
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(5.2=100)
A:
NA
C2:
PF0095516=HCO3_cotransp=PD(8.1=58.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCGATGCCCGTGCTCTA
R:
TGAGTGGGAAGACAATGGCTG
Band lengths:
236-461
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types