RnoINT0138476 @ rn6
Intron Retention
Gene
ENSRNOG00000020138 | Slc4a3
Description
solute carrier family 4 member 3 [Source:RGD Symbol;Acc:3712]
Coordinates
chr9:82751173-82751726:+
Coord C1 exon
chr9:82751173-82751391
Coord A exon
chr9:82751392-82751636
Coord C2 exon
chr9:82751637-82751726
Length
245 bp
Sequences
Splice sites
5' ss Seq
AAGGTACTC
5' ss Score
7.46
3' ss Seq
AACTTGGCTGCCTTTGGCAGGCT
3' ss Score
4.33
Exon sequences
Seq C1 exon
GTGTTCACAGAGCATCCTTTGCTGCCCTTCTACCCACCGGAGGAGGCCCTGGAGCCTGGCTTGGAACTGAATAGTAGTGCCCTGCCCCCCACAGAGGGACCACCAGGTCCCCGGAACCAGCCCAATACAGCTCTGCTGTCCCTCATCCTCATGCTGGGGACTTTCCTCATTGCCTTCTTCCTGCGAAAGTTCAGGAACAGCCGCTTCCTGGGGGGCAAG
Seq A exon
GTACTCTGTTCCCTTGGTTCCTATTGTCCCTGCTAAGCTCAGCTCCTGAGAGAGCCTTCCTCCCTTCTTGGCCTATCCATTGGCCCAACAGCCCCACCCCCACCCACCAGAAGACAGGAGTGCCTCCCAGCTGTGACTGGCGCATGGGCTGGCACACAGGCTGGCACAGCTTAGTCCCAGAAAGGGTTGGGGGGGGTGTCTCCTGTCCCTTAGCCTCTTGCTTCCAACTTGGCTGCCTTTGGCAG
Seq C2 exon
GCTCGGCGCGTCATCGGGGACTTCGGCATTCCCATCTCCATCCTGGTGATGGTCCTTGTGGATTACTCTATCACAGACACCTACACACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020138:ENSRNOT00000027337:17
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=0.000
Domain overlap (PFAM):
C1:
PF0095516=HCO3_cotransp=PD(12.2=32.9),PF0095516=HCO3_cotransp=PU(19.7=80.8)
A:
NA
C2:
PF0095516=HCO3_cotransp=FE(9.7=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:
CTTTGCTGCCCTTCTACCCAC
R:
CTGTGTGTAGGTGTCTGTGAT
Band lengths:
293-538
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]