DreINT0150747 @ danRer10
Intron Retention
Gene
ENSDARG00000037517 | slc35c2
Description
solute carrier family 35 (GDP-fucose transporter), member C2 [Source:ZFIN;Acc:ZDB-GENE-030131-2202]
Coordinates
chr23:20552536-20552954:+
Coord C1 exon
chr23:20552536-20552694
Coord A exon
chr23:20552695-20552784
Coord C2 exon
chr23:20552785-20552954
Length
90 bp
Sequences
Splice sites
5' ss Seq
AGAGTAGGT
5' ss Score
4.84
3' ss Seq
ACTGTGTCTTTTGTGAGAAGGAA
3' ss Score
3.87
Exon sequences
Seq C1 exon
GTGTGAAAAATGCAGATGAGGCAGAGTTGAGGCAGGTGGCGTCTGAACCTCTGGAGCTGAATGTGTATAAGGTGAATGATTTTCCTCTGCTCAGTAAACTGGTGGGAAAACTAGCACGCATCCTCTGTGGCAAGATTGAAGACCGTATTAAAGCCAAGA
Seq A exon
GTAGGTCAATCACAAATTTGTTTTCATTAAATTGGCGAATCTGTACCGTACACTCACATTAAAACTAAAAACTGTGTCTTTTGTGAGAAG
Seq C2 exon
GAATGGAGCATCCAACTCAGGAACCAGTTCTGTCATTTCCCAGCCCAACTGATCTGCAGTATGTAGGACTGGGCTCCAGAGAGTTGCGTCTGCGCTGGACCGTCCCCAGCAGAAATCCCCAGCAATACAGAGTGGTTTACCACACCGCTGAAGGACAGAGCCTTAATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000037517:ENSDART00000132920:18
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.056 A=NA C2=0.246
Domain overlap (PFAM):
C1:
PF0009223=VWA=PD(21.4=68.5),PF0385310=YjeF_N=PD(30.6=48.1)
A:
NA
C2:
PF0004116=fn3=PU(53.8=75.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGCATCCTCTGTGGCAAGATT
R:
ATTGCTGGGGATTTCTGCTGG
Band lengths:
169-259
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]