RnoINT0138479 @ rn6
Intron Retention
Gene
ENSRNOG00000020138 | Slc4a3
Description
solute carrier family 4 member 3 [Source:RGD Symbol;Acc:3712]
Coordinates
chr9:82742972-82743566:+
Coord C1 exon
chr9:82742972-82743114
Coord A exon
chr9:82743115-82743400
Coord C2 exon
chr9:82743401-82743566
Length
286 bp
Sequences
Splice sites
5' ss Seq
CAGGTGACT
5' ss Score
6.6
3' ss Seq
AGAGGTTATCTGGTCTGCAGGTC
3' ss Score
5.12
Exon sequences
Seq C1 exon
GCTCCCCAAGAGGTCTCCGCAGCGCCCCCTTCTTCTCACCCAGGATTTGGGTCCCGTAGTGACTGAGAGACTCCTAAGTCTTCAGCCCAACCATGGCTAATGGGGTGATCCCACCGCCCGGGGGCGCCTCCCCCCTACCCCAG
Seq A exon
GTGACTGATGCGTGGGGGTGGGGTGGGGGGGGAGGGGCAGGATGGGTGGGGTGTCCTCTGGATGACCCTGGGATTGGTGGTGTAGAGGAATAGGTGGTCTTTGGTATTTCATGCATTTGTAGCTGTGATGCTCCCAAGGCCTGGGGCAAGTCCTCAGAGGGCGTTTTGGGGATTTTGATGCAGGCAAGAGTGGAGGGGTTGGGAAGGCCCTTGAAGTATGGAGTTGGGGGTGGGTGGGGAGTGTTCATGAACTAGGGATACTTAGGAGAGGTTATCTGGTCTGCAG
Seq C2 exon
GTCCGGGTGCCCTTGGAGGAGCCCCCACTGGGTCCAGATGTAGAAGAGGAGGATGATGACTTGGGCAAGACCTTGGCTGTGAGCAGGTTTGGGGACCTCATCAGCAAGACCCCGGCCTGGGACCCTGAGAAGCCTAGCCGCAGCTACAGCGAGCGCGACTTTGAGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020138:ENSRNOT00000027337:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCCCCAAGAGGTCTCCGC
R:
CAAAGTCGCGCTCGCTGTAG
Band lengths:
305-591
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]