HsaINT0153537 @ hg19
Intron Retention
Gene
ENSG00000113073 | SLC4A9
Description
solute carrier family 4, sodium bicarbonate cotransporter, member 9 [Source:HGNC Symbol;Acc:11035]
Coordinates
chr5:139742030-139742651:+
Coord C1 exon
chr5:139742030-139742117
Coord A exon
chr5:139742118-139742496
Coord C2 exon
chr5:139742497-139742651
Length
379 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGC
5' ss Score
8.69
3' ss Seq
TTCTGTGCCCCCATTCCCAGCAA
3' ss Score
6.63
Exon sequences
Seq C1 exon
GTTTTTCTGCCTTCTCCTGGGCCCCTGTATGCTGGGAAAGGGCTACCATGAGATGGGACGGGCAGCAGCTGTCCTCCTCAGTGACCCG
Seq A exon
GTGAGCTGAGCAGGTGTGTGTGTGTGCGCGCGCACGCGTGCATGCCTGTGTGTGTGTGCACACATGCATACATGCATGGGCTCATGTGAGTGTGTGTGTGTGGACTCTGTATGTGTCCCTAAATACAGCAATGAGGCACAGTGAGCACTGAGACTGAAGTTTCCTCGTCTCCTAGTGCAGCCCCATTACTGGATGAGTGCTGGCACACTGTAGGCACTCAATAGATACCCACTGAATGAATGAATTAATGCATGCATAAAGGAATGTGTGAATGACTTGTCTGCCTCTGTGACTTGTGTCTGTCTAGTTTTGAGACTATGAAAATGCATGTAAGAGACCAGGTTTGCACTTACCACCCATTCTGTGCCCCCATTCCCAG
Seq C2 exon
CAATTCCAGTGGTCAGTTCGTCGGGCCAGCAACCTTCATGACCTTCTGGCAGCCCTGGATGCATTCCTAGAGGAGGTGACAGTGCTTCCCCCAGGTCGGTGGGACCCAACAGCCCGGATTCCCCCGCCCAAATGTCTGCCATCTCAGCACAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000113073-SLC4A9:NM_031467:6
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=0.250
Domain overlap (PFAM):
C1:
PF075658=Band_3_cyto=FE(21.0=100)
A:
NA
C2:
PF075658=Band_3_cyto=PD(26.1=69.2)
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:
GTTTTTCTGCCTTCTCCTGGG
R:
TTTGTGCTGAGATGGCAGACA
Band lengths:
241-620
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)