RnoINT0138473 @ rn6
Intron Retention
Gene
ENSRNOG00000020138 | Slc4a3
Description
solute carrier family 4 member 3 [Source:RGD Symbol;Acc:3712]
Coordinates
chr9:82749898-82750542:+
Coord C1 exon
chr9:82749898-82750116
Coord A exon
chr9:82750117-82750393
Coord C2 exon
chr9:82750394-82750542
Length
277 bp
Sequences
Splice sites
5' ss Seq
TAGGTGAGG
5' ss Score
7.65
3' ss Seq
CTGACCCCTTTCCACCCCAGGAG
3' ss Score
9.3
Exon sequences
Seq C1 exon
AACTGTCTTTGGAGATGGGAGGCTCCGAGGCAACCTCTGAAGATGATCCCCTGCAGCGGACAGGCTCAGTGTTTGGGGGGCTAGTACGGGATGTGAAGCGCCGGTACCCACACTACCCCAGTGACCTACGGGATGCACTGCACTCTCAGTGTGTGGCTGCCGTGCTGTTCATTTATTTCGCAGCCCTCAGCCCTGCTATTACCTTTGGGGGTCTGCTAG
Seq A exon
GTGAGGCTCTAGGGGTCACCGTGGGGGACAGATGTCACCTGTAGGGTTCTATGGTTCACATCACTCAGAGGGTCAATGGACAGAGGGGAATAAGAAAGCCACAGGAAGCTATTGAGCCAGAGGACTCAAGTGATCCATTTTCGGGGTGCCATAAAATGGGGGTGTAAAGGCAGAATCCCTGTAGTTTCCTTGGGGATGTGAATGGTTCCTTGTCTGTTAGTCTGGGAGCTAGATGAGGAAGGGAACAGGCTATCTCGCTGACCCCTTTCCACCCCAG
Seq C2 exon
GAGAGAAGACTGAGGGGCTGATGGGTGTGTCAGAGCTGATTGTGTCCACGGCTGTGCTTGGGGTTCTCTTCTCTCTGCTGGGGGCCCAGCCGCTGCTCGTGGTGGGCTTCTCTGGCCCTCTGCTGGTCTTCGAAGAAGCTTTCTTCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020138:ENSRNOT00000027337:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.162 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0095516=HCO3_cotransp=PU(28.9=77.0)
A:
NA
C2:
PF0095516=HCO3_cotransp=FE(24.9=100)
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:
TGTCTTTGGAGATGGGAGGCT
R:
CCCCCAGCAGAGAGAAGAGAA
Band lengths:
300-577
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]