HsaINT0153296 @ hg19
Intron Retention
Gene
ENSG00000004939 | SLC4A1
Description
solute carrier family 4, anion exchanger, member 1 (erythrocyte membrane protein band 3, Diego blood group) [Source:HGNC Symbol;Acc:11027]
Coordinates
chr17:42335354-42335991:-
Coord C1 exon
chr17:42335781-42335991
Coord A exon
chr17:42335549-42335780
Coord C2 exon
chr17:42335354-42335548
Length
232 bp
Sequences
Splice sites
5' ss Seq
TAGGTACCT
5' ss Score
4.67
3' ss Seq
GCTCTTATCCTCCACCACAGACT
3' ss Score
7.04
Exon sequences
Seq C1 exon
GTGTTCCGCATAGATGCCTACATGGCTCAGAGCCGAGGGGAGCTGCTGCACTCCCTAGAGGGCTTCCTGGACTGCAGCCTAGTGCTGCCTCCCACCGATGCCCCCTCCGAGCAGGCACTGCTCAGTCTGGTGCCTGTGCAGAGGGAGCTACTTCGAAGGCGCTATCAGTCCAGCCCTGCCAAGCCAGACTCCAGCTTCTACAAGGGCCTAG
Seq A exon
GTACCTGCCCTTCCCAGCTGAGGCTTTCTGAGCCCCCACCGACCCCCAGACACCTCAGCGTAGCCTCTGTCTCCCATCACATGTTCCCCTCTCATCGCTCCCTTTGCCCACATCTTCCAGACTTCTTCGCCGCCCCATTCCCATCAGACAATCTCCCCTACACCCTCCAGTCCCCTTTCCCCTCACCTCCTCCAGCTACTCCCTCTGACCATGCTCTTATCCTCCACCACAG
Seq C2 exon
ACTTAAATGGGGGCCCAGATGACCCTCTGCAGCAGACAGGCCAGCTCTTCGGGGGCCTGGTGCGTGATATCCGGCGCCGCTACCCCTATTACCTGAGTGACATCACAGATGCATTCAGCCCCCAGGTCCTGGCTGCCGTCATCTTCATCTACTTTGCTGCACTGTCACCCGCCATCACCTTCGGCGGCCTCCTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000004939-SLC4A1:NM_000342:10
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.028 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF075658=Band_3_cyto=PD(14.8=50.7)
A:
NA
C2:
PF0095516=HCO3_cotransp=PU(29.1=86.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTAGAGGGCTTCCTGGACTG
R:
GATGAAGATGACGGCAGCCAG
Band lengths:
307-539
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)