HsaINT0153536 @ hg38
Intron Retention
Gene
ENSG00000113073 | SLC4A9
Description
solute carrier family 4 member 9 [Source:HGNC Symbol;Acc:HGNC:11035]
Coordinates
chr5:140362017-140362532:+
Coord C1 exon
chr5:140362017-140362174
Coord A exon
chr5:140362175-140362444
Coord C2 exon
chr5:140362445-140362532
Length
270 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
GGGCCTGGTTCCTTCCTCAGGTT
3' ss Score
8.51
Exon sequences
Seq C1 exon
TGTCAGAACCCCCTGAGACAGAAGCTACCTCCAGGAGCTGAGGCAGGGACTGTGCTGGCAGGGGAGCTGGGCTTCCTGGCACAGCCACTGGGAGCCTTTGTTCGACTGCGGAACCCTGTGGTACTGGGGTCCCTTACTGAGGTGTCCCTCCCAAGCAG
Seq A exon
GTGAGGCTACTGAGTGAGTGGGAGTCAGGGATCCCAGAACCTAGAAGGGTCTTTACTGAGGAGGGGAAGGAGGGTCTCAGTCTGATTCTCTGAGGCTGTGGGGAGGATGGTGCTCAGGGGTCTGGGGAGAGAGTAGTGGTCAGGGCTGCATGGTAGGTGTGCAAATGAGTGTGTTTATGGGAGCTGATAGGTCAGAGCTGAGCATCAGAGGCCAGGGCTGCCCTGTGGGAAAGCAGCCTGTGAATCTCTGGGGCCTGGTTCCTTCCTCAG
Seq C2 exon
GTTTTTCTGCCTTCTCCTGGGCCCCTGTATGCTGGGAAAGGGCTACCATGAGATGGGACGGGCAGCAGCTGTCCTCCTCAGTGACCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000113073:ENST00000506757:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.170 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF075658=Band_3_cyto=FE(37.7=100)
A:
NA
C2:
PF075658=Band_3_cyto=FE(21.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGTCAGAACCCCCTGAGACAG
R:
GGTCACTGAGGAGGACAGCT
Band lengths:
244-514
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains