DreINT0150785 @ danRer10
Intron Retention
Gene
ENSDARG00000037517 | slc35c2
Description
solute carrier family 35 (GDP-fucose transporter), member C2 [Source:ZFIN;Acc:ZDB-GENE-030131-2202]
Coordinates
chr23:20513815-20514957:+
Coord C1 exon
chr23:20513815-20513990
Coord A exon
chr23:20513991-20514827
Coord C2 exon
chr23:20514828-20514957
Length
837 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGA
5' ss Score
8.68
3' ss Seq
TAATATGCTTCTCTCTGTAGGAG
3' ss Score
9.98
Exon sequences
Seq C1 exon
GACTGAGTGTGAGCACCACAGAGAAGCTGTTCAGGGTCAGTGAGCTCTCTCACCTGCTGTACTCTTTAGTCACTCTGTCTGTGGGTGGCATGCTGGCGTTCGGGCTCGGCTTCTCTGAGTTCCTGCTGGTGTCACGCACGTCCAGTCTTACACTGTCCATTGCAGGCATTTTTAAG
Seq A exon
GTGAGAACAAATGCAGTCAAACCAAAATTTGCTCAGACCCTAGATAGATTTTTACTTTTTTTTTCTTACGGATGCTAAACATTTTATAGTATAGTGTAAAATGCTGAAGTAGAAATGCACTAAAGTTAATATTCCCAGTCAAAACGGAAATTGGATGGACTTTCGCCATAAACCTAAATGAAAAAAAGTTCATCTTGACCAATAGCCATCATTTTACCAGTGTTGCCATGACAGCATAGTAACGCACATGCAAGCAGCAGGAACAAGTATACTACATAGAAAAGTCCTTCCGGTGCATTATTTGAGCCCAGCAGTGATCAGTGTGGCATAGTATAGCCTTTTTACCCCGTCTCGTATTTTCAGCCAACTTTCTCTTTCAGTTGAAACATATTTTTTGTCGATCATTTTTGGTAGCCCAAAATTTGGTGGATCCCTATACTAAAGTTCAGGTTTAAATGAGTCCTTGAGACTTATGCTGCACAAACAAAGTGTTTATATTCTCAAACTAACAGCTATTTGAATAATTTTTGGGATTGTAATCCATTAAATCCTGTCTGTCAAAGTTATTAGAAATTTATTACATTTATTATTATCATGATGAATTTTTTCTTGAATTGAGTTCTGTTAACATTTTCCTAACTGTAGCTAATTAACTGTCATAATGTGACAGGTTGATTATGTTTAATTTGACACTGTTATTTTTGCATACTTGCAGTATAAGAAGCTGCTGAAGCACTGTCTCGTCCTCTTTCTGTTTTTGGTGATTTTTCCCTAATAGCTCAGCGTGGTATTAAAGTCTTCATTAGTCTAATAGTGTTAATATGCTTCTCTCTGTAG
Seq C2 exon
GAGGTGTGCACTCTGCTGCTGGCAGTGGAGTTCTTGGGGGATAAAATGAGCACAGTCAACTGGCTTGGTTTTGCTGTGTGCCTGTCTGGGATATCACTTCATATTGGCCTAAAAACATACCGTAACAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000037517:ENSDART00000132920:8
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:
PF065706=DUF1129=PD(13.1=22.0),PF0315111=TPT=FE(38.4=100)
A:
NA
C2:
PF0315111=TPT=PD(23.2=79.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Mouse
(mm10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GACTGAGTGTGAGCACCAC
R:
TGTTACGGTATGTTTTTAGGCCA
Band lengths:
303-1140
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]