HsaINT0153458 @ hg19
Intron Retention
Gene
ENSG00000188687 | SLC4A5
Description
solute carrier family 4, sodium bicarbonate cotransporter, member 5 [Source:HGNC Symbol;Acc:18168]
Coordinates
chr2:74449995-74452122:-
Coord C1 exon
chr2:74451967-74452122
Coord A exon
chr2:74450080-74451966
Coord C2 exon
chr2:74449995-74450079
Length
1887 bp
Sequences
Splice sites
5' ss Seq
GAGGTGGGG
5' ss Score
4.41
3' ss Seq
TTCCCACTGTTTTTCTCCAGCCC
3' ss Score
9.4
Exon sequences
Seq C1 exon
ATCCTGGGCCTCATCATCGTTCGAAGGCTTCTGGATTTCATCTTTTCCCAGCACGACCTGGCCTGGATTGACAACATCCTCCCAGAGAAGGAAAAAAAGGAGACAGACAAGAAGAGGAAGAGAAAAAAAGGGGCCCACGAGGACTGTGATGAGGAG
Seq A exon
GTGGGGAAGATGTGAGGCCGGGGCACAGAGGAGAAATTGAGAGACCTTCTCTCCACTTTTGCCAGGGACAGGGAGAGGGCGGCTTCTTGGGTGGCCTGCAGCAGTGCCTCGGCCCAGTCCAGGATGGGCTGGGGCATCTGCTTGTCTTGGTCTGGGGTGTTGAGGGCTCTTCTGTTTATGTGAATATCCTCAGGGTGGGCCAGAGTGAATGAGACTCCCTGTCCAGGGAAAAGGTGACTGGCCATGCCCACTCTTTCCATCACTGTGGGCTTTACGGCCGTGATCACAGCAAGCGGGTTCCTGTGGGAAGGGCCAGGAGGCAGCTCCAGCATGGAAGGAGGTTATGAAGACTGACCTCCAAAGAGTGGAGCAGACTTGGGGAGAGGTGTCTAATGGGGCCTTATAAGTAGACTGGACTCCAGACAGGCAGGAGGGGCTGGGAACAAGTTTTGCTTGCGCCTTTGCCTAGGGTATTGAGGACAAAGATGGGGAAAGAGGCAGGTATCCTCGCCAAAAGGAGACTGGCTACATTTCCCAGATGTCTGGGACAACATGGTTGCCCCATCTGCCCCTCTTCTCCCATGGTCCCTTCCCATTTCATCCCCAAAACACTCAGGGAGTCAACAGACAAGGGGCCAGTCCAGAAATTATAGTGAATCACAAAACATGAGGCAGAAAGATTCTTAATTCATGTGTTCATTACTTATGATGAAACTGTCCCCACAAAAGGAAGTGACTTACCCAAAATGGACATGTAGCTACATTTCTAAGAAGGAATTAAGAAAATAATTCCTGACTTTGCTGGTTTCTGATATGCTAAGCTGCCTGTGCCATCTCCTAATGCTGTGCTTGGTTCCCAATCTCCCAATTTGACCCAAACTCACGTCCCTGCATCCACCCTGTCCTGTTCTCGTGATTTTGCCTTGTGCAGATGAAACCTGTTCAAGGCAAATCCCTTCTGACTGGCTGGTGGTGATTAAACCATCTTCTGATCAGTCAGAACTCCCCTGGTCCTTAATTACTGTGCTCTTCCAGGAAGAGTCCCATAATGCATGTGTTTGTAGATGATTTGTAAAGGTGGGTTCTGAAAACAAAGAAACAGAGACTAAGTGCCTTTTAAAGACAAATACTTCTTTTGTTGATACTTTCAATAAATATCTGAGTGGCTACCACATGCCAAGAACTATTACAGGGTTGGGAAAAAGAATCTCTGAATTATGATATATCAATGGAAAAACAGGATTCAATTTATACAAATTCATTTTACTTGTCTTATAGCAACACAGTTGTTGTGTGAGGTTCATTCCCAAGTGACTGGTTGCTGTGACAGATAAAACTGTTTTGATGAGTAACATTCCTGGAAGAGTTCCGGTCTGTCTGATGGTGTGTATAGGACAGCAGGCTAACTGTGCCCATTCCCCTTCAGTGGACCCCAGGGTATTTGCAGCATCCCCTAACTGTTTAGAGGTGAACAGAATGGTGGTTTGCAATGTTCATGCATGCATTTTCCATCTTGGCAAGAAAGCCAAGTTGTTGGCCACGCGCGGTGGCTCACATCTGTAATCCCAGCACTTTGGGAGGCCGAGGCAGGGGGGATCACAAGGTCAGGAGTTCAAGACCAGCCTGGCCAGCATGGTGAAACCCCATCTCTACTAAAAATACAAAAAATTAGCCAGGTATGGGGGTGCACGCCTGTAATCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATCACTTGAACCCAGGAGGCAGAGGTTACAGTGAGCCGAGATCGCACCACTGCACTCCAGCCTGGGCAGTAGAGCGAGACTCTGTCTCAAAAAAAAAAAAAAAGAAAGCCAAATTGTTGTGTTGGTGTTTATCCTCTTTTCCCACTGTTTTTCTCCAG
Seq C2 exon
CCCCAGTTCCCTCCTCCCTCGGTTATAAAGATTCCCATGGAAAGTGTCCAATCAGATCCCCAAAACGGTATCCACTGCATTGCCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000188687-SLC4A5:NM_021196:24
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.409 A=NA C2=0.092
Domain overlap (PFAM):
C1:
PF0095516=HCO3_cotransp=PD(1.9=17.3)
A:
NA
C2:
NO
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:
ATCCTGGGCCTCATCATCGTT
R:
GGCAATGCAGTGGATACCGTT
Band lengths:
240-2127
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)