BtaINT0135361 @ bosTau6
Intron Retention
Gene
ENSBTAG00000003635 | SLC35C2
Description
solute carrier family 35 (GDP-fucose transporter), member C2 [Source:HGNC Symbol;Acc:HGNC:17117]
Coordinates
chr13:75804318-75805098:-
Coord C1 exon
chr13:75805026-75805098
Coord A exon
chr13:75804487-75805025
Coord C2 exon
chr13:75804318-75804486
Length
539 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGG
5' ss Score
8.3
3' ss Seq
CCCCCGCCCTCTGCTTTCAGCGC
3' ss Score
11.99
Exon sequences
Seq C1 exon
GTACACGATGACCAAGTCCTCAGCCGTCCTCTTCATCCTCATCTTCTCTCTGATCTTCAAGCTGGAGGAGCTG
Seq A exon
GTGAGGCCCCAGCTTTCCTCGAGTCCCGCCAGCCCCCACCGATGCTAAGAATAGAAAGCGGGAGCTGCTCAGTGTCTTGTCCCTGCCTGTGACCAAGGAGGCAAGCCCAGCTCAGTGGCACTCCATCCCTGGGGACAGACCCGGGGCGCTGCTGGAGAAGATTTAGGGACTGGTGTGGCAGGAGCGGTGACCACAGGAGATGGGGTTCAAGGACGTGGGACTGGGGCAGTGGGTCCTGGGGGCTCCCTGCTGTGCAGCTGGGGCCCTTCATGTGCTGGGTCCAAGGGGGCGGTGGGGCCACGTGGGGCCATAGGGCCGTTGTAGGACAGCCCTACTGCCCTGTTTCAGGGTCTGGGGTCCATGCCAACCAGGTGTCAGCCCTGGTAACATCGAGTGGAAGGGACCAGCCAGGACCCCAGGGTGGGGCAAGAAGAAGGAGGCCTTGCCCCAGGGGCAGCCAAGATGGTCACTGGCCCCCAGTCTCCCAGGCGTGATGAACCCAAGTTGATTGCAGTTGCTCCCCCGCCCTCTGCTTTCAG
Seq C2 exon
CGCGCGGCGCTAGTCTTGGTGGTCCTGCTCATCGCCGGGGGCCTCTTCATGTTCACCTACAAGTCGACGCAGTTCAACATCGAGGGCTTCGCCTTGGTGCTGGGTGCCTCTTTCATCGGCGGCATTCGCTGGACCCTCACCCAGATGCTCCTGCAGAAGGCGGAACTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000003635:ENSBTAT00000039194:6
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:
PF084496=UAA=FE(19.0=100)
A:
NA
C2:
PF084496=UAA=FE(44.4=100),PF0315111=TPT=PU(75.7=49.1),PF0315111=TPT=PU(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Mouse
(mm10)
No conservation detected
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CACGATGACCAAGTCCTCAGC
R:
CAAGTTCCGCCTTCTGCAG
Band lengths:
239-778
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development