RnoINT0138488 @ rn6
Intron Retention
Gene
ENSRNOG00000020138 | Slc4a3
Description
solute carrier family 4 member 3 [Source:RGD Symbol;Acc:3712]
Coordinates
chr9:82746826-82747500:+
Coord C1 exon
chr9:82746826-82747006
Coord A exon
chr9:82747007-82747364
Coord C2 exon
chr9:82747365-82747500
Length
358 bp
Sequences
Splice sites
5' ss Seq
AGGGTAGGG
5' ss Score
5.76
3' ss Seq
TTTCCCTCACTGTGTCCTAGGAG
3' ss Score
9.01
Exon sequences
Seq C1 exon
GTGTTCGTGGAGCTGAATGAACTGATGTTGGACCGGAGCCAGGAGCCACACTGGCGGGAGACAGCACGCTGGATCAAGTTCGAAGAGGATGTGGAGGAGGAGACAGAGCGCTGGGGGAAGCCTCATGTTGCTTCGCTCTCCTTCCGTAGCCTCCTGGAGCTTAGGAGGACCATTGCCCAGG
Seq A exon
GTAGGGCTCCTTGGGCTGGCCCTTCTCCCCACCGTAGCTCCATCTGTGTTGGGCTGCCCAGTGTGCCGGGATCATTTGGGGAATTCTGAGGGGCAGGACTACACATTGCACCTGGGCCTAATGGACGGCCTTCTAGCTGTCTGCACTCTTAGGGTATGACTCCCATTGCTCGGCTCCTTGTGCCTCAGCCCCTCGCACACCATTTTCCATATGCTCCTCCAGATGCCTGTGAGGTGTGTAACTGCTGTTAGTGCATTGGCCCTCAGCTCACTTTACACATTGGCCTGCCCTTGGGGAGCAAGGTAGTGGGGTGGGCCTCCCTTCTGGCCGGACGGCTCTTTCCCTCACTGTGTCCTAG
Seq C2 exon
GAGCGGCTCTCCTGGACCTGGAGCAGACCACCCTGCCGGGCATCGCTCACCTTGTGGTGGAGACCATGATTGTATCTGACCAGATCCGGCCCGAGGACAGGGCTAGCGTTCTGAGAACTCTGCTCCTGAAACACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020138:ENSRNOT00000027337:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.082 A=NA C2=0.130
Domain overlap (PFAM):
C1:
PF075658=Band_3_cyto=PU(11.5=50.8)
A:
NA
C2:
PF075658=Band_3_cyto=FE(16.7=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:
TCGTGGAGCTGAATGAACTGA
R:
TGTGTTTCAGGAGCAGAGTTCT
Band lengths:
312-670
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]