HsaINT1042116 @ hg38
Intron Retention
Gene
ENSG00000113073 | SLC4A9
Description
solute carrier family 4 member 9 [Source:HGNC Symbol;Acc:HGNC:11035]
Coordinates
chr5:140364054-140364625:+
Coord C1 exon
chr5:140364054-140364187
Coord A exon
chr5:140364188-140364362
Coord C2 exon
chr5:140364363-140364625
Length
175 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGA
5' ss Score
9.79
3' ss Seq
CCTGTCTCTCATCCCCACAGAGA
3' ss Score
11.99
Exon sequences
Seq C1 exon
GGAGTGCTGGAAAGTTTCCTGGGCACAGCAGTGGCTGGAGCTGCCTTCTGCCTGATGGCAGGCCAGCCCCTCACCATTCTGAGCAGCACGGGGCCAGTGCTGGTCTTTGAGCGCCTGCTCTTCTCTTTCAGCAG
Seq A exon
GTAGGAGAGCTCCCCCCATCACCGGACCCTCACTAGTGCCATGGTCAGCCTGCTCCTGGCTGGGTGAATAGGAGAGAGTGGGAGCTATCTGTTTGGGTTGAGGGACACCTGACCTGGGTTTAGTGGGAAGCAGACAGCCCTGCTAAGCCAGCCTTCCTGTCTCTCATCCCCACAG
Seq C2 exon
AGATTACAGCCTGGACTACCTGCCCTTCCGCCTATGGGTGGGCATCTGGGTGGCTACCTTTTGCCTGGTGCTGGTGGCCACAGAGGCCAGTGTGCTGGTGCGCTACTTCACCCGCTTCACTGAGGAAGGTTTCTGTGCCCTCATCAGCCTCATCTTCATCTACGATGCTGTGGGCAAAATGCTGAACTTGACCCATACCTATCCTATCCAGAAGCCTGGGTCCTCTGCCTACGGGTGCCTCTGCCAATACCCAGGCCCAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000113073:ENST00000506757:10
Average complexity
IR
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(21.3=100)
A:
NA
C2:
PF0095516=HCO3_cotransp=FE(17.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTCACCATTCTGAGCAGCAC
R:
GTTCAGCATTTTGCCCACAGC
Band lengths:
253-428
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains