DreINT0150783 @ danRer10
Intron Retention
Gene
ENSDARG00000037517 | slc35c2
Description
solute carrier family 35 (GDP-fucose transporter), member C2 [Source:ZFIN;Acc:ZDB-GENE-030131-2202]
Coordinates
chr23:20512585-20512955:+
Coord C1 exon
chr23:20512585-20512753
Coord A exon
chr23:20512754-20512871
Coord C2 exon
chr23:20512872-20512955
Length
118 bp
Sequences
Splice sites
5' ss Seq
TTGGTAAGT
5' ss Score
10.47
3' ss Seq
TCCCACTCTTTGACACCCAGGTC
3' ss Score
6.07
Exon sequences
Seq C1 exon
AATCCATTCCTGATCCTGGTGGTTGTCCTGATTTCCAGTGGTCTCTTCATGTTCACTCTCAAGTCCACTCAGTTTAATCTGGAGGGTTTCATCATGGTCCTGTTAGCCTCTTTTATCGGAGGAATCCGCTGGACTCTCACTCAGTTGCTCATGCAGAAAGCAGAGCTTG
Seq A exon
GTAAGTCTTTAGTGTGAGCAAGGATGGTGGATGCTCCTGTTAAGTTCCCTTAACTTTGTTTGTGTTCATTCTGTGTTGAATTTTGCATGACTCTCCTGTCCCACTCTTTGACACCCAG
Seq C2 exon
GTCTTCAGAACCCCATAGACACCATGTACCATCTGCAGCCCCTCATGTTCCTTGGCCTATTTCCCTTGTTTCTTCTTAATGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000037517:ENSDART00000132920:6
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:
PF0089215=EamA=PD(13.7=33.3),PF065706=DUF1129=FE(56.6=100),PF0315111=TPT=PU(18.5=49.1)
A:
NA
C2:
PF065706=DUF1129=FE(28.3=100),PF0315111=TPT=FE(18.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCCATTCCTGATCCTGGTGGT
R:
AGAAGAAACAAGGGAAATAGGCCA
Band lengths:
243-361
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]