MmuINT0147292 @ mm10
Intron Retention
Gene
ENSMUSG00000024485 | Slc4a9
Description
solute carrier family 4, sodium bicarbonate cotransporter, member 9 [Source:MGI Symbol;Acc:MGI:2443384]
Coordinates
chr18:36530276-36530868:+
Coord C1 exon
chr18:36530276-36530363
Coord A exon
chr18:36530364-36530713
Coord C2 exon
chr18:36530714-36530868
Length
350 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGT
5' ss Score
10.9
3' ss Seq
TTCTGTGACCTTAAATGCAGCAA
3' ss Score
5.05
Exon sequences
Seq C1 exon
ATTTTTCTGCCTCCTCTTGGGTCCTCCCACCCTGGGAAGGAGCTACCATGAGATGGGACGGGCAGCTGCTGTCCTCCTCAGTGACCCG
Seq A exon
GTGAGTGGGCCAGGGTTTCCTCTGTGTGTGTATGTGTGTGCATGTGTGGAACATATGTATGGGCTTTGTGTATGTGGTCAGGAATAACAGTGAGGCAGAGTGTGGCTTTGTTTTTGTACCATGGGGGCTGAAGTTTCCAGTTCACTGCTGGCCCAAGGTAGACACACATAGGCACAAATTGAATGAATGGATGGATGGATGGATGGATGGATGGATGGATGGATTTGTGAGTAAATCATGATTTGTCTGCTTGTAGCCTGTGTGAGGATGGCTTTGAGAAAATACAGGTGAACACACATGGAAGAGTCCTTAATATGCACTTCCCGTCCATTCTGTGACCTTAAATGCAG
Seq C2 exon
CAATTCCAGTGGTCAGTTCGTCGGGCAAGCCATCTTCCTGACCTTCTGGCAGCTCTGGATGCCTTCCTGCAGGAGGTGACAGCTCTACCCCCGGGCCGGTGGGACCGGACAGCCCGGATTCCCCCACCCAAATACCTACCATCTCAGCACAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024485:ENSMUST00000074298:6
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=0.067
Domain overlap (PFAM):
C1:
PF075658=Band_3_cyto=FE(20.7=100)
A:
NA
C2:
PF075658=Band_3_cyto=PD(25.7=69.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTTCTGCCTCCTCTTGGGTCC
R:
CTTTTGTGCTGAGATGGTAGGT
Band lengths:
240-590
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