HsaINT0153427 @ hg19
Intron Retention
Gene
ENSG00000080493 | SLC4A4
Description
solute carrier family 4, sodium bicarbonate cotransporter, member 4 [Source:HGNC Symbol;Acc:11030]
Coordinates
chr4:72412067-72413437:+
Coord C1 exon
chr4:72412067-72412245
Coord A exon
chr4:72412246-72413364
Coord C2 exon
chr4:72413365-72413437
Length
1119 bp
Sequences
Splice sites
5' ss Seq
GAGGTGTGT
5' ss Score
6.14
3' ss Seq
ATCTTTTGATTTGGTTTCAGGGA
3' ss Score
8.33
Exon sequences
Seq C1 exon
AAAGGAGCAGGGTATCACTTGGATCTCTTTTGGGTGGCCATCCTCATGGTTATATGCTCCCTCATGGCTCTTCCGTGGTATGTAGCTGCTACGGTCATCTCCATTGCTCACATCGACAGTTTGAAGATGGAGACAGAGACTTCTGCACCTGGAGAACAACCAAAGTTTCTAGGAGTGAG
Seq A exon
GTGTGTTAACTCAGAGGAAAATGGCTCCCGAAAACACACTGTGCACACATCTATGTGGCAATCATAAGGATATGGGCAGATTTGGAGGAGACAGGGCTTGTGATGATTAATTTATTCCTATATTTTTTGTTCCAGAAAGGACTAAATTTTCATCAGAGGTTTCAGTGATTTTTTTAGTTTACTCCTCATGATATATCATTTTCATGGATTTCCAAAAGGCTAAATGTTGCAATATAAAACTACAACCAGATTACTTTTTTTCAACATGCAGGTGATTTTGGTGCTGCAGTGTTTACTGTATCACAGTCATATGTGAAGGCCCTAAAACTCTTGAGTCTGCTTATGACTTTTAAGATTCTGTAATGGGAAAGGTATTCTTATTTTCCAATTCATTTTCTGTCCCCATAAACACTGAGAAACTTTAACCTCCAGACGTTCAATTTGGGTAGCTGTGAAGGGCAGGAGTAGAAGGTTTTTATACTCTGTTGAGCACTTTTTACAGCAAACTCTGCTCATAAGTGCTTGGGTAGAGAGCTCACATGACAGAGCCATCGTTTCCCACGGCAAAACAGTGGGTGATTCTTTTTTGGGGTGGGGAGGGGGTGTAGGATGGGAATTATATTTGTTGAAAAGTACTTTTGTTGTTGTAGATTTGGAAATTAGACTGATGTGATTTATTGTGCTAATGAAATTTCCTTGAGCTGTTTGTTAATTGGAATATGGGACAATGTAATATCTGTCTCCTATGAAAGAAGGTGTAAGGGTAATTACACAAGAGGATAAATTGCTTTAAAAAATAAGGTCTTCAAAGAGTCCAGTAATTGATGGACCAAGAGCAAGTGATTTTTCTTTCTTGATTCCAAAAGGAGCAAAAAATTTAGCAGGATTACTTCTTTCTTCGTGAATTCAAATCACATATTGCAGTCACTTTAAGAGATTTTTTTATAGTTACGTTGGGTTTATACGCTATCCTTGAGGTATTATTTACATGATATCAACACCTTTGTTGTTTTAGCCAAACATTGATTTTGTCAATGTGTAGTTTTTTTGAAGGTGAAAAGACAAGAGCATGTTTATGAAGACAAGAGGTAGATTGGTAATCTTTTGATTTGGTTTCAG
Seq C2 exon
GGAACAAAGAGTCACTGGAACCCTTGTGTTTATTCTGACTGGTCTGTCAGTCTTTATGGCTCCCATCTTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000080493-SLC4A4:NM_001098484:19
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(11.3=100)
A:
NA
C2:
PF0095516=HCO3_cotransp=FE(4.6=100)
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:
AAGGAGCAGGGTATCACTTGGA
R:
AGATGGGAGCCATAAAGACTGAC
Band lengths:
246-1365
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)