HsaINT0153412 @ hg38
Intron Retention
Gene
ENSG00000114923 | SLC4A3
Description
solute carrier family 4 member 3 [Source:HGNC Symbol;Acc:HGNC:11029]
Coordinates
chr2:219630072-219632116:+
Coord C1 exon
chr2:219630072-219630352
Coord A exon
chr2:219630353-219631967
Coord C2 exon
chr2:219631968-219632116
Length
1615 bp
Sequences
Splice sites
5' ss Seq
AGAGTGAGT
5' ss Score
7.36
3' ss Seq
CAAGCCCATCTTCTCTGCAGGTC
3' ss Score
8.58
Exon sequences
Seq C1 exon
GCCGTGCTCTGAGCTGAGGGACGGTGATGGAACCACCGACCTGGCCCTGTCAAGTCCAAGGCTGCTGTGTTGCCTCCCCAGCTCCCCCAGCCCCCGGGCCCGGGCCTCCCGACTCGCTGGGGAGAAAAGCCGGCCCTGGAGCCCATCGGCCAGTTATGACCTGCGGGAGCGACTGTGCCCAGGCAGTGCCCTGGGCAACCCAGGTGGTCCAGAGCAGCAGGTGCCCACAGATGAGGCGGAGGCCCAGATGCTGGGTTCTGCAGACCTGGACGACATGAAGA
Seq A exon
GTGAGTGAGACCTTGTGGCAGCCCCCATGGTCCACTGCGACGGACTCCCAGCCTGCGAGTGACCTTGGAGAGGCTCTGAGCTGTCCCCTGCTAAGGGCTGAGTCCTCTCTGAATCCCTGTCTGCTGGGATGTGGCCAGTGATGGGGACCTCACTACCTCACCCAGCCACCCTCTCTGACGGCCAGAGCTGAGATTTCCTTTCCTGACACCTCACGCCTCAGTCCTGATTCTGTCCTCTGAGTCACCCCTAGAAAAAGGCAGCTCTCTTTTTCACATTACTGTATCCCTCCCCAAGGCCCCTCTTCTCGGGGTGAACTCTCTGTCTCCTCTTTGATCCCCTCCAAACCAGGCCCTGAGTCTGAGCCATTGCTCCGGACCCCTGCCTCTCCCTGTGTCAGGACCCTTCACTCCCATCCCACTACCCTTGGGGGGGGCCTGGCTGTGATCTCGGCACATTCCTTCCATCTTATCAGTGCCCTGGTTTCTGTGCCACCTGTCATCACCCGTGGGGCTCTGTGCCCAGGCCAGGGGCATCACTGATCCCTCCCCCTCCTCCGAGCCACAGTGTGTGGGTGGGGTGGGGGGAAGGGTAGGGCTTTGAGCTCAATACGTCATGGAAAGTTGCCAGGGCCTGAGGACAGGGACAGGAACAATCCGATGGCAGCAGTAGCAGCAGGATGGGGGGTGGGGGAGGGCGTGTTTACAGACCCAGGGTGGGGGCTGGATGCCGCAGGGAGCAGGCTTGTGGACTTGGGGAGTTGGGGTCGGGAGGCTGTGCCACCTTCAGCTCTGGTTGGACAGAAGCCACCCCGTCCAGGCTCCCACCTTGTAGGAGAGCCGAGGGGTCTGGTAGGGAGCGGAGGCCGAGGTCTCGGCCACCGGGAGAATGACGAGCCCACTGGAGAAGGACCCTGAGCCCAATGGGGCACTGAGCCCTGGGCCTGGGGATACCAATAGCTGGGGCTTTGGGAGGGATCCAGCCCCCAGTCCTCGAGACTCACTGGCCCCGGAAGACTTAGAGATGTTTGTGCTGGACTTTGAGGATGGTGACCTGTGGGAGTCCATCAGGGGCCAGCTGGGCCCCATGGCAGGGCCACCAACTTGTGAGTAACGGGGCTGCTGGCCTTTCCCCGACTGCTGCTGGCCTGGGTGGGGCAGACAGGAGGAAGGGAGCGAAGCCCTGCCTGAGTCTACTGGGCTGTGTACCTTCGGGGAGGGGACGTGGGTGTTGAGATAGGGTGCACGGAAAATGTTGGGGGCTCAGTGCCTGGGGACTCTGACTCAGTGCCTGTCATGGGACCCAGATGGAGAAGGAGGGGCAGTGGCCATGGCAGGGGCTGGAGGGTCTGGCTGGGGCTGTGGACTGAGCTGGGTCTACCTTTGGATTGCATCTTGGCCGGTGGTCCCAGGTGACCATGGGGAGGTCCTTCCCTCTTTCTGAGCTTCAGTCTTCTTATCAATGAAATGGCCACATGGGATTATGTGGTTCCCGTCGGCATGGCCTGTTGGTGACTGTAGAGCTCACCAAGTAGATGGGTTGGGCAGAAGGAGCTGGGCCGTGACCCCGAGGGCCCCAGCTGGACCTGTGGGACCCCCAAGCCCATCTTCTCTGCAG
Seq C2 exon
GTCACCGACTGGAGGACAACCCTGGTGTGCGGCGACACTTAGTGAAAAAGCCCTCCCGGACGCAGGGCGGGAGGGGCAGTCCCAGCGGCCTGGCCCCCATCCTTCGCAGGAAGAAGAAGAAGAAAAAGCTGGACCGGAGGCCTCATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000114923:ENST00000273063:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.851
Domain overlap (PFAM):
C1:
NO
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:
AAGTCCAAGGCTGCTGTGTTG
R:
CTTCTTCCTGCGAAGGATGGG
Band lengths:
346-1961
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