DreINT0150750 @ danRer10
Intron Retention
Gene
ENSDARG00000037517 | slc35c2
Description
solute carrier family 35 (GDP-fucose transporter), member C2 [Source:ZFIN;Acc:ZDB-GENE-030131-2202]
Coordinates
chr23:20556046-20558191:+
Coord C1 exon
chr23:20556046-20556175
Coord A exon
chr23:20556176-20558045
Coord C2 exon
chr23:20558046-20558191
Length
1870 bp
Sequences
Splice sites
5' ss Seq
CATGTGAGT
5' ss Score
7.83
3' ss Seq
TAAATCCTCTTCTCTTTTAGTAC
3' ss Score
8.43
Exon sequences
Seq C1 exon
CTGGTGGTGAATGGAACAGAGTCCACAACTCTGCTGACAGGACTGTCCTCACAAACACAGTACCATCTATCCATCTTCCCCGTCTATGAGAATAAAGTGGGCTCCGCTCTCAGAGGCACCTTCACCACAT
Seq A exon
GTGAGTTTCAGCTTAGTCTATATATAAAATGTATTCAGATATTTCTCAAGTGCTGTTTCATGGAGCTGAGTTTTTTCAACACATTTTAAACAATAATTCACTAAAAACTCATTTTTAGCCCATCATTGAGTCTATTTATTTAGTTGTGTTAATGTGTGTAAAATTTATATTTATTCAGTTTTTAAATAAATTTAACTAATATTATTGTTATATAATAATAGTAATGTTAAAATGTTCATATGATTTATTTACAATACAGTTTGTAAATTATGTTCTGTTTCTTACCAGATATATTATATAAGAGGCTTGCTTTGTTTACCAAACAAGTGGATCTAATTGGGTTTGCATTGTAAACATTAAATAAAAGTAAAAAATGTTTTATTTTTATTGTATATTTTAAGTTTTAGTTATGATACTCCCAAAATCATTTTTACAAAATTCTGTGTGAAATAGCAAAAAATGTCTGGCACTACTAATAATTCTAATTCCTACTAATTCTTTTGTGTTTGACATGATAACAATACATACGAATTTATTAAGATACTAGTGGCTTAAAGTGGCATATAAAGTCTTAACTAGGTCAACTAGATACGTTAGGTTAATTAGGCAAGTCGGACAACATTGGGTTTTTTTCTGTAGCCAATCAAAAAATAATATTAATCTTAAGGGACCTAAGAATATGGACTTTACCTCTTTATTTTATACATTTTAACTGTATTTTTTGTTCAAGGCAAACTTTAAAAAATAAGATTTTTTCCTGAAATAAAATAAATATGTAATAGTGAAAAAAAAAATCCAATTACTGAAAAATGCTTTGAAAATATATCCTTTTTTATCCTTGCTCAATTGGGAATTATTTTTAAAAGAATTGCAATTGCAAAAGAGGCTAATGATTTTGTTTTCAAATCTGTTGTTAGGACTCTGGTCTAGGGTGACAAGGATGTAATATAAAAACCACTGGACAAATAAAATCACTTTTAAGAACCCTTGGGGTGGGCTCAGTTTATTTGTTAGTTTTATTCTTTTTCTTTTTCAAACACCCAAAATGTGAAGCCAAATAGCCACAGAAAAAAATAAACAAGAAATATCGCCTATCTATACACCCAAATAAATACATACATCTAACAAAATAACAGAAATAAAATACAAAACTACATCTGTCTTTCTAACGATATATAAAAACAAGAGAAAATATTTACAGAAAAGAAAAGTGTGGCATCCAACTCCTACTGCTTCTCACCGTGTATATACAAAGTACAGTACTTACAATAACAACAAACAAACCCAAAACAAAATTACAAAGGGGGAACACAGATGGTTAAACAACAAACAAACAAAAGTCAAACTTTACACTCACACAAACCAGGAATACACAATCAAAAAAATAACACATGCAGCTATATTTTTCTACTGCACCAAATGCCAAACAACACGCCAAGCAACCCGCTCTCTCTAGCTCCACACTTGTTCCACTTTTTAAAAAGCGTTCTGGGTCACTCCAGCCAATCCCAGAGTACGTCGCCAGGCGTAATTAGGGTGGGGCTTGTGGAGAGAGAGAGAGAGAAAAAGAGAAAGAAGGCGAGGGGGGGAAACGAGACACACATACACTTGCGAACGCAACACTATATACAGTGTTGATAGTTTAAAATCCCAAGACCAAACTGATCTGCAGTTTAAAATTAGGGAAACCGAAAATTCTGTTTCTTGCCTGTACACCTGGCACTTATAAATTATTTTTAATTTGACACATTACATTTGTTTGTCTGTTAAATGCATACAAAATCTTGCTGGTCAAGTGCAGCTGACTTTAAAACAGAAAGGGGAAAAGTAATTTTGAAACTGTGCTATAATAAATCCTCTTCTCTTTTAG
Seq C2 exon
TACCGTTGGCAATCCCTGAGGCTCTGGAGGTCACAGCCTCCTCTGCCAGCAGTCTGCGGGTGCGCTGGCAGCCGGCTGCTGGAGCCACACAGTACATGGCCTTATACTCAGCACTCAATGATGGAGAGCCTGATGATGCCAAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000037517:ENSDART00000132920:20
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.023 A=NA C2=0.082
Domain overlap (PFAM):
C1:
PF0004116=fn3=PD(43.8=79.5)
A:
NA
C2:
PF0004116=fn3=PU(54.9=91.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCCACAACTCTGCTGACAGG
R:
CTTTGGCATCATCAGGCTCTCC
Band lengths:
254-2124
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]