HsaINT0153517 @ hg19
Intron Retention
Gene
ENSG00000050438 | SLC4A8
Description
solute carrier family 4, sodium bicarbonate cotransporter, member 8 [Source:HGNC Symbol;Acc:11034]
Coordinates
chr12:51852343-51853892:+
Coord C1 exon
chr12:51852343-51852434
Coord A exon
chr12:51852435-51853734
Coord C2 exon
chr12:51853735-51853892
Length
1300 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGC
5' ss Score
9.6
3' ss Seq
TGTTTCTTTTGGACTTTCAGGTA
3' ss Score
10.02
Exon sequences
Seq C1 exon
GTCAAACCGTGTCTCCTCAGTCTGTTCCAACTACAAATCTTGAAGTAAAAAATGGAGTGAATTGTGAACATAGTCCTGTGGATTTAAGCAAG
Seq A exon
GTGAGCAGAGTGGTGGGAAGTTGGCTTCAAGGCCTAAGGTTCCTTTTAGTGGAATCCAGAGTTTAATTGCTGGAATCTGGGTAAGGTTTAGTGTTTCAAGACTCTTTCCCTAAGACTAGAGCCCTTTCTGCATAAAAGGGGGCCCATCTCTGCATGTCTTTTCCCTTCTCCTTCAGCCTGGATGAAGCTGACTCAACAGTTTCTTTCTCCAGATTCAACATACTGAAAACTGGGACTAGCTGCTTAGAATCTTCCCTAAAACAGATCTCTTGATTTTTCAATTATTTTTTTGGTACCTGCTCTCCAGCAGTTCCTTCTCACCCCCAGGGGTTTTGCCAAAACAATATTTTGGATATCTATTTAGAGACAGATGTCTCCTAAAACTAACTCTTGGTTGAAGCTCTCCTTGAGGACTGTGACTTTGGTATCTGAGGCCTTCTGTAGCAGCAGTGTCTCACTGCAGCTTATGGTCCAAGCCTTGGTCTCCCTGCCTCCAGCCTCTCCTTGCTCTGGTCTATCTTTGACACTGTGTTTCTAAAACACAGATAGTGTCATATCACTTCCTCTGCTCATAAGGCTTCCCATTTTATTTGGAAAACCTGAAACCCCCGACAAAACATTTGAGTGTTTAAAAAGGGAAAGAATGTGACCCAGAGCTTCAGAAACATTTCTCTTGGAGGAAGCTTGGGGGAATGGGATTGAAATCAGAATACCTGATTTTAAAATCCGAACCTATACCTTAAAAGCTCTGTGGTCCCGGGCAAGTCAACTTCACCTCTCTGGGTTTCAAATACTTCATTTTTTTTTTTTCTTTAAGTGGGACGAATACAATCTGTCATATCCTCCTTCTGGGGTTTTTGTAAGGATCAAATAAAATAAGAAAACATTTGCTAACCATAAAATGACATATGAGTGTAAGATATATTTTAGGTGATGGGGCCAGGTGCAGTGGCTAACGCCTGTAATCTCAGCACTTTTGGAGGCTGAGGCGGGTGGATCACATGAGGCCAGGAGTTTGAGACTAGACTGGCGAAAATGGCAAGACCCCATCTCTACTAAAAATACAGAAAAATTAGCTGGACATGGTGGTGCATGCCTGTAATTCCAGCTACTAGGGAGCCTGAAACACAAGAATTGCTTGAACCTGGCAGCAGAGAGCTGTGAGCTGAGATTGCGCCACTGCACTCCAGAGTGGGTGATGTAGTGAGACTCTGTCTCAAAAAAAAGTAAATAAAAAATTTAAAAACGATATTTAAGGTGGTGGTTCCCAAGTTGTCAGATGTTTCTTTTGGACTTTCAG
Seq C2 exon
GTAGACCTTCATTTCATGAAAAAAATTCCTACTGGGGCCGAGGCCTCCAATGTCCTGGTTGGAGAGGTGGATATTTTGGACCGTCCCATTGTTGCCTTTGTGAGGCTGTCTCCAGCTGTTCTTCTCTCAGGCCTAACAGAAGTGCCAATCCCAACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000050438-SLC4A8:NM_004858:7
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.613 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF075658=Band_3_cyto=FE(11.5=100),PF120133=DUF3505=FE(37.0=100)
A:
NA
C2:
PF075658=Band_3_cyto=FE(20.0=100),PF120133=DUF3505=PD(1.2=1.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCAAACCGTGTCTCCTCAGTCT
R:
TGTTGGGATTGGCACTTCTGT
Band lengths:
247-1547
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)