BtaINT0135363 @ bosTau6
Intron Retention
Gene
ENSBTAG00000003635 | SLC35C2
Description
solute carrier family 35 (GDP-fucose transporter), member C2 [Source:HGNC Symbol;Acc:HGNC:17117]
Coordinates
chr13:75800482-75801916:-
Coord C1 exon
chr13:75801741-75801916
Coord A exon
chr13:75800612-75801740
Coord C2 exon
chr13:75800482-75800611
Length
1129 bp
Sequences
Splice sites
5' ss Seq
AAGGTACAG
5' ss Score
8.04
3' ss Seq
CCCTGCCTCTCTTCCCGCAGGAA
3' ss Score
13.77
Exon sequences
Seq C1 exon
GTCTCCATTTGTCCACATCTGAGAAAATCTTCCGTTTCCAGGACACAGGGCTGCTCCTGCGGGTGCTCGGGAGCCTCTTCCTTGGCGGGATTCTCGCCTTTGGTTTGGGCTTCTCTGAGTTCCTCCTGGTCTCCAGGACCTCCAGCCTCACTCTCTCCATTGCTGGCATTTTTAAG
Seq A exon
GTACAGTCTTGGAGGCGACCCCAGTCCTGTCTTAGAGGGGAGCCCCTCTCCGGTGGGTGTCCCAACTCCTGCTTCCCAGAGCCCTGCAGGGAAGAAACGGAAGTGCCTGTCTCATCTGGCAGTCAGTCCATCATCATCACGGCCCAGAGTGGGGGTGGGGGGGTGGCGGGGGGGGGGGCAGCCCTGCTTCACAGATGGGGAAACAGACATGAAGAGCTGCCCTTACCCAGGGATATACAGCTAGCAGGTGGCCGAGCTGACTCCACTAGGCCTGGGACGTGTTTACATCTTACCAAGAAAGCCAACTCTAGTCATTAGGCAGTGGCCTGGAGTCAGGATTGAGAAGTCCCCAGTCAGACTCATCAGCATAGGGTCCTGTGCTTGGCAGTGATTGATTGACAGTGTCTGCCAGGAGCACAGTGAGGGGTGGTTCTATCACGAGGGCCCTGCGGCTGCTGATCCTGCCTTTACCGCTGTCTAGGAGCCCCTAGCCGTCTCCTTGCATCACTTCTCCCCTTCTTCCCCCCATCATCACTCACTGCTTCCTGCTCTGGGCTGTGGACAGGCAGATCCTGATCCTGGAGCAGTGTTCCCTGAAACCAGCCGAACAGGGCTCCCTGAGGGTCTCGCCCACCCAGTGATGACACGTGAGCCGTGTTTCTCAAAATGTCATCTGATCAGTCCCCTTTGCAGCCCGTGCTTACGAACAGCCCTGTGACCAGTGTGTCCCGTAGAGCCCAGTGTGACTGCACCCACCCCCACCCACGGCAGCAGAGGCGCTCCGTGCACAGGTGCTTCTGGAAGGGCAGCTGTCCTTCCTGCCTGTGGACGTGGCTGCGGACTTGCTACCCTGTGTCCCCAGCCTGGATTCGGTCTGTCTCTTCCAGTCCGGACAGAATTCTGTGAAAAGCACCTCCCCTCTGTCCACAGTAACACAGAGCAGGGGAGGCCTCACGCTGGTCCCCAAACTCAGAGAGGCCTACCCCTTTGCATTGCAGGGAGTTTGGGCAGGTCTGCCTCTCCCCTGCGGTGTGACGGCTGACGGCGGCCCCAAGCCCCACCTTCCTTTGCAAGGAGCGTCCCCCGCCTTGGCCCTGAGCACGCCCCCTCCCTGCCTCTCTTCCCGCAG
Seq C2 exon
GAAGTCTGCACTTTGCTGTTGGCCGCGCATCTTCTGGGTGACCAGATCAGCCTCCTGAACTGGCTGGGCTTTGCCCTCTGCCTCTCAGGAATATCTCTGCACATCGCCCTCAAAGCCCTGCATGCCAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000003635:ENSBTAT00000039194:8
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:
PF084496=UAA=PD(7.9=16.9),PF0315111=TPT=PD(21.6=13.6),PF0315111=TPT=PU(61.1=98.3)
A:
NA
C2:
PF0315111=TPT=PD(36.8=79.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCTCCATTTGTCCACATCTGAGA
R:
CTGGCATGCAGGGCTTTGAG
Band lengths:
304-1433
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development