BtaINT0130774 @ bosTau6
Intron Retention
Gene
ENSBTAG00000018307 | SEMA3F
Description
sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3F [Source:HGNC Symbol;Acc:HGNC:10728]
Coordinates
chr22:50737748-50738122:-
Coord C1 exon
chr22:50737983-50738122
Coord A exon
chr22:50737863-50737982
Coord C2 exon
chr22:50737748-50737862
Length
120 bp
Sequences
Splice sites
5' ss Seq
CTGGTACGA
5' ss Score
7.84
3' ss Seq
CTCCTGCCCACCCCCACCAGAAT
3' ss Score
6.45
Exon sequences
Seq C1 exon
ACCCTTCTTTCATCCACGCCGAGCTCATCCCTGACAGTGCCGAGCGCAACGACGACAAGCTCTACTTCTTCTTCCGTGAGCGGTCCATAGAGGCGCCGCAGAGCCCTGCCGTGTACGCCCGCATTGGGCGGATCTGCCTG
Seq A exon
GTACGAAGCCCCTTTGCTGCCCCCTGCCCAGGCCCAGTCCTGGCTCTTGTCAGCCCGGCTTTGGCGGGGTCTTGGGGGTGAGCGAGCTGATCTGACTCAGCTCCTGCCCACCCCCACCAG
Seq C2 exon
AATGATGACGGCGGCCACTGCTGCCTGGTCAACAAGTGGAGCACATTCCTGAAGGCAAGGCTGGTCTGCTCTGTGCCAGGCGAGGATGGCATCGAGACCCACTTCGACGAGCTCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000018307:ENSBTAT00000024362:8
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:
PF0140314=Sema=FE(9.7=100)
A:
NA
C2:
PF0140314=Sema=FE(8.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTTCTTTCATCCACGCCGAG
R:
GAAGTGGGTCTCGATGCCATC
Band lengths:
243-363
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]