BtaINT0130762 @ 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
chr22:50735427-50736373:-
Coord C1 exon
chr22:50736151-50736373
Coord A exon
chr22:50735516-50736150
Coord C2 exon
chr22:50735427-50735515
Length
635 bp
Sequences
Splice sites
5' ss Seq
CAGGTACCC
5' ss Score
8.63
3' ss Seq
CCCTGCCCGGCCCGTTCCAGACC
3' ss Score
7.03
Exon sequences
Seq C1 exon
TGCCCTGGCGGAACCTTCACGCCGTCCATGAAGTCCACCAAAGACTACCCTGATGAAGTCATCAACTTCATGCGCAGCCACCCGCTCATGTACCAGGCCATCTACCCTCTGCAGCGGCGGCCCCTGGTGGTCCGCACAGGCGCGCCCTACCGTCTCACCACTGTGGCCGTGGACCAGGTGGACGCAGCCGACGGGCGCTATGAGGTGCTTTTCCTGGGCACAG
Seq A exon
GTACCCACTGCTGCTCCCAGCCCCTCCCACGCTGGGCCCGCTGGGTGGAGGGTGCTGACCCACAGGGCTGGGCCCTGACCTCCTAGGGGGTTGCTACAAGGTTGTCCCTGTCACCCCTGCCACCTCCTTCATCCTATGGAGCCCTCTATTACCAGGATAACTGAGAATGGGGGTGGGGAAACCCCATTCCCATCCTCATCCCTGGTGGCCGGGAGAATGGGGACCCAGGGTGCCTGGGGACCCATGTTTGGGCAGGAAGAGGGAAGACAGAGGCAGGCACTTCCAGGACACCCGGGTCCAAGCACACACATGCTCTCGTGTGCACATGCAGACCACATTCACCGCTGTCCCAGTAGTTGTCAACCCAGGGGAACGCATCCTGCATCCTGTTCTCAGCTTCCCAAACGAGGGTCTGGGGGCAGAGGGGCAGACTCTAGCTGTGGCACCCTCCTTATGCAGGGCCAGCCCCCTTAGACCTCTTCCCCTCATCTGGGGGCTGCTCTTCCACCTTGGCATAGAGCACGCCCACTCCACTGCCCCTGGGGGGTCTGGGCCCTGGTGGGGGAAGGGGCTGAGGCTGGTGCCCCTTTCCCAGCACCCTCAGCCCCGCTGAGGCCCTGCCCGGCCCGTTCCAG
Seq C2 exon
ACCGCGGGACAGTGCAGAAGGTCATCGTGCTGCCTAAGGACGACCAGGAGATGGAGGAGCTCATGCTAGAGGAGGTCGAGGTCTTCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000018307:ENSBTAT00000024362:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.147 A=NA C2=0.100
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(15.6=100)
A:
NA
C2:
PF0140314=Sema=FE(6.1=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:
CCCTGGCGGAACCTTCAC
R:
CTTGAAGACCTCGACCTCCTCT
Band lengths:
310-945
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]