HsaINT0153523 @ hg38
Intron Retention
Gene
ENSG00000113073 | SLC4A9
Description
solute carrier family 4 member 9 [Source:HGNC Symbol;Acc:HGNC:11035]
Coordinates
chr5:140365520-140366022:+
Coord C1 exon
chr5:140365520-140365578
Coord A exon
chr5:140365579-140365833
Coord C2 exon
chr5:140365834-140366022
Length
255 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGG
5' ss Score
7.61
3' ss Seq
CCTGACCCTCCTGTGTACAGGAC
3' ss Score
8.51
Exon sequences
Seq C1 exon
GAAATGAGTCTCAATGGATAAGGACAAGGCCAAAAGACAGAGACGACATTGTAAGCATG
Seq A exon
GTGAGGGACTGCTCCTGGGAGGTTCTAGGAAGGAAAGGGTGGAGACCAAGGCAGTCGGTGGTTTCTAGCTCTTCCTACCCATAGGTTAAGGAAACCTTCATAGGTGAGTAAAGCTTAGCCATTTCCTACAGCTGGGAACTTCCCATCCTGGGCCCCTGGTGTCTCTGTGGGTCCCTCCTCCCTTGAAGTTGGTCCAGGAGAGCAGGACATTTACTCCATTGCCTATAACTCCACTCCTGACCCTCCTGTGTACAG
Seq C2 exon
GACTTAGGCCTGATCAATGCATCCTTGCTGCCGCCACCTGAGTGCACCCGGCAGGGAGGCCACCCTCGTGGCCCTGGCTGTCATACAGTCCCAGACATTGCCTTCTTCTCCCTTCTCCTCTTCCTTACTTCTTTCTTCTTTGCTATGGCCCTCAAGTGTGTAAAGACCAGCCGCTTCTTCCCCTCTGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000113073:ENST00000506757:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.157 A=NA C2=0.063
Domain overlap (PFAM):
C1:
PF0095516=HCO3_cotransp=PD(4.3=45.0),PF0095516=HCO3_cotransp=PU(4.1=50.0)
A:
NA
C2:
PF0095516=HCO3_cotransp=FE(12.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGAGTCTCAATGGATAAGGACAAGG
R:
CACAGAGGGGAAGAAGCGG
Band lengths:
244-499
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