HsaINT0153400 @ hg38
Intron Retention
Gene
ENSG00000114923 | SLC4A3
Description
solute carrier family 4 member 3 [Source:HGNC Symbol;Acc:HGNC:11029]
Coordinates
chr2:219635271-219635891:+
Coord C1 exon
chr2:219635271-219635496
Coord A exon
chr2:219635497-219635672
Coord C2 exon
chr2:219635673-219635891
Length
176 bp
Sequences
Splice sites
5' ss Seq
AAGGTCAGA
5' ss Score
6.8
3' ss Seq
GCAGCCCCTTGTTCCCCCAGAAC
3' ss Score
8.05
Exon sequences
Seq C1 exon
CTGTTTCATGAGGCTGCCTACCAGGCAGATGACCGGCAAGACCTCCTAAGTGCCATCAGCGAGTTCCTGGATGGCAGCATTGTGATCCCCCCGTCCGAGGTGGAGGGCCGTGACCTGCTGCGCTCCGTGGCTGCTTTCCAGCGAGAGCTGCTTAGGAAGCGGCGAGAGCGTGAACAGACCAAAGTCGAGATGACCACACGGGGTGGCTACACGGCCCCTGGGAAAG
Seq A exon
GTCAGACCCTTGGAGGCTGAGTGCCCCCAATACACACTCCCCCATCCCAGGGCCCTAAGGCTGTGACCCCAGCCCCGTCCTGACTCCTGGAGTCCTTTGCATCCCTGATCCCAACAGCCCGGGGCCTCCGAGCCAGAGGGAGTGGTCTGTGCCCCAGCAGCCCCTTGTTCCCCCAG
Seq C2 exon
AACTGTCTTTGGAGTTGGGGGGCTCTGAGGCAACCCCTGAAGATGACCCCTTGCTGCGGACGGGCTCGGTATTTGGGGGGCTTGTGCGGGATGTGAGGCGCCGGTACCCGCACTACCCCAGTGACCTGCGAGATGCGCTGCACTCCCAGTGTGTGGCCGCTGTGCTCTTCATCTACTTCGCAGCCCTCAGCCCTGCCATCACCTTCGGGGGGCTGCTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000114923:ENST00000273063:13
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.164 A=NA C2=0.108
Domain overlap (PFAM):
C1:
PF075658=Band_3_cyto=PD(13.3=47.4)
A:
NA
C2:
PF0095516=HCO3_cotransp=PU(11.7=77.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGAGAGCGTGAACAGACCAAA
R:
TGAGGGCTGCGAAGTAGATGA
Band lengths:
253-429
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains