HsaINT0153527 @ hg19
Intron Retention
Gene
ENSG00000113073 | SLC4A9
Description
solute carrier family 4, sodium bicarbonate cotransporter, member 9 [Source:HGNC Symbol;Acc:11035]
Coordinates
chr5:139747305-139748244:+
Coord C1 exon
chr5:139747305-139747483
Coord A exon
chr5:139747484-139748171
Coord C2 exon
chr5:139748172-139748244
Length
688 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
ACTCCTCCCTCTCCCCACAGGGA
3' ss Score
14.61
Exon sequences
Seq C1 exon
AAGGGAGCTGGCTTCCACCTGGACCTCTTCTGTGTGGCTGTGCTGATGCTACTCACATCAGCGCTTGGACTGCCTTGGTATGTCTCAGCCACTGTCATCTCCCTGGCTCACATGGACAGTCTTCGGAGAGAGAGCAGAGCCTGTGCCCCCGGGGAGCGCCCCAACTTCCTGGGTATCAG
Seq A exon
GTGAGGGCGGTATTTAGGAAGTGGAGTAAGAGGTGGGCAGCAAGGTAAGGCAAAGGGGAACATGGCAGAGTTACTTGGGCAGCTTAAATTCTAAGCTGGTGTCCCACAAGCATTGCAGTGGCAGAATGAGTGAGTTCTGGGCTCTGAGATGGGTGAGTCAGATCTTCCCCTCTCTCCCCTCAGCCATGGGGACTGGGAGGGGCCTCAAGAGGATTATCATCCATGCAAAGGTAGAGGCAGCCAGGGCTGAAGTGGAGGGTCAGGTGCCACCTAATAATCCTCACTCAATGTAGAAGTTACAAAGGAATCCATCATAAAAGCAATTTTGGAACTGTTGGAAGCACAGTCTAAGTATCTAAAGTATATGAAATCAACTTGATAAATTGTGAAATGTAAGTCTTTATGGCAGTGTAAACATTGCTAATTTTCCATCAAAATAAAAATAAGGAGCAACTATGAACTTGAATTGATGGAGAGGTCTGGGACTCTCACCTTGAAGTGCTCTGCCCCTTCCTCTCCACCAATTTTTCACATCAAGCTAAGGGCTCATCCCTCTGGGTGACCTACTGGGGTATTCCTCTAGTTTTCTCTTGCTGCCGGGGTCTGTACTGGTATTCAGCCAGGATCTCCAGTCTGGATACCCCAGGGACTCTCCCAGACCTCAGCTAACTCCTCCCTCTCCCCACAG
Seq C2 exon
GGAACAGAGGCTGACAGGCCTGGTGGTGTTCATCCTTACAGGAGCCTCCATCTTCCTGGCACCTGTGCTCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000113073-SLC4A9:NM_031467:16
Average complexity
IR-S
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(11.5=100)
A:
NA
C2:
PF0095516=HCO3_cotransp=FE(4.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAGGGAGCTGGCTTCCACC
R:
CACAGGTGCCAGGAAGATGGA
Band lengths:
246-934
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)