DreINT0150744 @ danRer10
Intron Retention
Gene
ENSDARG00000037517 | slc35c2
Description
solute carrier family 35 (GDP-fucose transporter), member C2 [Source:ZFIN;Acc:ZDB-GENE-030131-2202]
Coordinates
chr23:20547393-20547998:+
Coord C1 exon
chr23:20547393-20547560
Coord A exon
chr23:20547561-20547878
Coord C2 exon
chr23:20547879-20547998
Length
318 bp
Sequences
Splice sites
5' ss Seq
TAGGTAGGA
5' ss Score
7
3' ss Seq
TTAATTTGTTATGGTTTTAGCGC
3' ss Score
7.03
Exon sequences
Seq C1 exon
CTGTTTCCACACGAAAGCCATTTGAATGCAGTGCTGAGGCTCAGGCGGAACTGGTCCTGCTGGTGGACGGATCCTGGAGCATCGGTCGGACAAACTTCAGAAAAGTGAGGGAGTTCCTTCAGGGCCTTGCTGTCCCCTTTCACATCGGCCCAGAGGGCGTCCAGATAG
Seq A exon
GTAGGAGATTGTATTTAATGGTTATGTGCTTCAGTCTCAACATTCATACCCCATTCTTCAGTGTCACATGATCTTTTAGAAGTTCTTTAAATATGCTGAATTGAGCTCAATAAACATTTTTATTATCATCAGTTTTTATTTATTTATTTTTTCGAAAATATTTTTTAAAATGTGACACTTTTTGAAGGCTTTTCATGAATACAAGTTAAAAGTACATAGTTTGTTTATAAAAAAGAAAGCTTTTAGAACACAAATGCCTCTTGATTTAATGAATGAATGCCATTGGTGGTTAAAATTATTAATTTGTTATGGTTTTAG
Seq C2 exon
CGCTGTCTCAGTATAGTGGAGATCCACGCACAGAGTGGCATCTTAACAACTTCACATCAAAAGAGCCGCTCCTGGAGGCCGTCAGGAACTTCAGATACAAAGGAGGGAACACTTTTACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000037517:ENSDART00000132920:15
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.175 A=NA C2=0.171
Domain overlap (PFAM):
C1:
PF0009223=VWA=PU(23.1=70.2)
A:
NA
C2:
PF0009223=VWA=FE(23.1=100),PF0385310=YjeF_N=PU(3.5=7.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGTTTCCACACGAAAGCCAT
R:
TGTAAAAGTGTTCCCTCCTTTGT
Band lengths:
287-605
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]