HsaINT0153414 @ hg19
Intron Retention
Gene
ENSG00000114923 | SLC4A3
Description
solute carrier family 4, anion exchanger, member 3 [Source:HGNC Symbol;Acc:11029]
Coordinates
chr2:220496984-220497731:+
Coord C1 exon
chr2:220496984-220497164
Coord A exon
chr2:220497165-220497595
Coord C2 exon
chr2:220497596-220497731
Length
431 bp
Sequences
Splice sites
5' ss Seq
ATGGTAGGG
5' ss Score
5.88
3' ss Seq
GTGCCTGACTGTCCCCCTAGGAG
3' ss Score
9.84
Exon sequences
Seq C1 exon
GTGTTCGTGGAGCTGAACGAGCTGATGCTGGACCGCAGCCAGGAGCCCCACTGGCGGGAGACGGCCCGCTGGATCAAGTTTGAGGAGGACGTGGAGGAGGAGACGGAGCGCTGGGGGAAGCCCCATGTTGCCTCGCTCTCCTTCCGTAGCCTTCTGGAGCTCAGGAGGACCATCGCCCATG
Seq A exon
GTAGGGACCCCCAGGCCTGGCCCGAGGCTGCAAGCCCTCTTCAGTCTGTGCCAGGCTGCTCAGTTCCCAGGAACACTCTCTAGAGTCCTGGGCACAGGCAAGATCCAACTGCCACCTGGGACCGTGGGGGTCCATTTGCCTGGGCAGCCCGTGAGCCCCGAGGGGCAGGGCTGTATCTGGTGCATGCAGTCAGTCAACAAATGGCTTCCCCTTCCTTGGTGGGGAGGGGCCGTGCCCTCGTTTCCATGCTCCATTTTCACGGCCCCTCTCTGACTGGCCTGTGGCAATATGGAGCTGTGTATCCATCTGGGTACATTGGGCGCTTTGCCCTTCCAGCACATTCGCATGCTTTTGGGGGGCAAGGCAGAGTGGGAGGAGATTTTTCCTGTCTGATGGGACTGTGCCCTCTCTGTGCCTGACTGTCCCCCTAG
Seq C2 exon
GAGCTGCCCTCCTGGACCTGGAGCAAACCACCCTGCCAGGCATTGCACACCTCGTGGTGGAGACCATGATTGTGTCTGACCAGATCCGGCCGGAGGACAGGGCCAGCGTCCTACGTACCCTGCTACTGAAGCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000114923-SLC4A3:NM_005070:8
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.111 A=NA C2=0.125
Domain overlap (PFAM):
C1:
PF075658=Band_3_cyto=PU(11.5=50.8)
A:
NA
C2:
PF075658=Band_3_cyto=PD(57.9=95.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGTTCGTGGAGCTGAACGA
R:
TCAGTAGCAGGGTACGTAGGAC
Band lengths:
310-741
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- 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)