HsaINT0153539 @ hg19
Intron Retention
Gene
ENSG00000113073 | SLC4A9
Description
solute carrier family 4, sodium bicarbonate cotransporter, member 9 [Source:HGNC Symbol;Acc:11035]
Coordinates
chr5:139743024-139743487:+
Coord C1 exon
chr5:139743024-139743140
Coord A exon
chr5:139743141-139743312
Coord C2 exon
chr5:139743313-139743487
Length
172 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
TGACGACCCTCGGGCGGGAGGCT
3' ss Score
-5.99
Exon sequences
Seq C1 exon
GCTTCCCTCGCAACAGCGGGAGATCAGAGGTCCCGCCGTCCCGCGCCTGACCTCGGCTGAGGACAGGCACCGCCATGGGCCACACGCACACAGCCCGGAGTTGCAGCGGACCGGCAG
Seq A exon
GTGAGGCGAGCTGGGAGGAAACAAGGGTAGGTGACCTGGGGGAGGGGAGGAGTCACAGGGAAACTGAGGTGTGTGCTCACTGTGGGAGGGGCTCACCCGGTCACAGGGAAAGTAGCGGGGATGCGGGTGTGGAGTGTGAAAACCTGGATCACTGACGACCCTCGGGCGGGAG
Seq C2 exon
GCTGTTTGGGGGCCTTATCCAGGACGTGCGCAGGAAGGTCCCGTGGTACCCCAGCGATTTCTTGGACGCCCTGCATCTCCAGTGCTTCTCGGCCGTACTCTACATTTACCTGGCCACTGTCACTAATGCCATCACTTTTGGGGGTCTGCTGGGAGATGCCACTGATGGTGCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000113073-SLC4A9:NM_031467:8
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.838 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0095516=HCO3_cotransp=PU(1.2=15.0)
A:
NA
C2:
PF0095516=HCO3_cotransp=FE(11.3=100)
Main Inclusion Isoform:
NA
Other Inclusion 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:
AACAGCGGGAGATCAGAGGTC
R:
GACCCCCAAAAGTGATGGCAT
Band lengths:
252-424
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)