RnoINT0137272 @ rn6
Intron Retention
Gene
ENSRNOG00000018170 | Slc27a1
Description
solute carrier family 27 member 1 [Source:RGD Symbol;Acc:620927]
Coordinates
chr16:20009193-20009500:+
Coord C1 exon
chr16:20009193-20009354
Coord A exon
chr16:20009355-20009430
Coord C2 exon
chr16:20009431-20009500
Length
76 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGT
5' ss Score
11.01
3' ss Seq
AACGTCTGCTTCTTCTGCAGATC
3' ss Score
10.71
Exon sequences
Seq C1 exon
CGGTGGCGGAGGTGAGTGAGCAGCTGGGGAAGAGCCTGCTCAAGTTCTGCTCTGGAGATCTGGGGCCTGAGAGCGTCCTGCCTGACACGCAGCTTCTGGACCCCATGCTTGCTGAGGCGCCCACCACACCCCTGGCACAGGCCCCAGGCAAGGGCATGGATG
Seq A exon
GTAAGTGGAGGGGTCCCTGACATTTATCCCCTCTGTCCTTGGCATTCCTGGTGCACAACGTCTGCTTCTTCTGCAG
Seq C2 exon
ATCGGCTATTTTACATCTATACTTCTGGGACCACCGGACTTCCTAAGGCGGCCATTGTGGTGCACAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000018170:ENSRNOT00000024659:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0050123=AMP-binding=FE(12.4=100)
A:
NA
C2:
PF0050123=AMP-binding=FE(5.3=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:
GGGAAGAGCCTGCTCAAGTTC
R:
GTCCGGTGGTCCCAGAAGTAT
Band lengths:
175-251
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]