BtaINT0130771 @ 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
chr22:50739807-50741626:-
Coord C1 exon
chr22:50741534-50741626
Coord A exon
chr22:50739901-50741533
Coord C2 exon
chr22:50739807-50739900
Length
1633 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGC
5' ss Score
8.07
3' ss Seq
CGCCCCTCTCTGCCCTGCAGGAT
3' ss Score
11.54
Exon sequences
Seq C1 exon
GCCACTCCCTGGACCCAGATGCAGGTGGTCAGAGGCCGAGGCAGCAGAGCCACCGATGGCGCCCTCTACCCGACGCCCACAGCCCCACGCCAG
Seq A exon
GTGGGCCTCATCCCTCCAGGCCCTTGCCAGCCAGTACTGCCTCAGCACCGAACTCACCCTGGGCCTGACCTTCCAGCCAGGAACCCGCACCCCAGGCCAGCCTCCCCAGGGTTTTCTGTCTACCTGTGTGCCCCCTCCCACCCCTTTCCCTGCAGTGCCCTCAGGCTCTGAAGGCATTCCCAGTTGGACTCGTGTCAGCCTCAGTGTGACGAGAAATCATGAAGTCACCAGTTGGGGAAAACAGGAGCCCTGGGGACAGCCATCCCTCCACCCTCAGAACACGTGTGTAGACATGTGTGAGCACATACCAACATACGCGTGGGCACGCGTAGGGCACTCTCCAGCCCACACCTTACTCAGCACCCAGTGCGGGAATATGGCGCGTATGTTCAGCCTGACGTAGCTCTCAGGGGTTCGTGCCCCAGGCCTCCCTGGTCGTGCATTAATGCAGGTGTCCTGCATACCCCCATGTCCGGGGTGGAAGGGGCAGAACTGTGTTTCTACTAGGCTTGACCTGGGACAAGGCTGGGCTGGGGGGCACTGGAGGGAGGGGGCACTGGGGGCCGGGGCTGGGGGGGGCCGGGGCTGGGCAGGGGCGGGCAGGGGGGCAGAGGCTGCCGGTGAGTGACAGAGCAAGTGGTCACTTGAGCTGGTGTGTCTGTGGCAGGGAGTGCTGAAAGGTGGGACCGCTCAGACTGTGTGTGTGCGCTCCCAGGGTGTGAACAATGGGTTCCGTGTGTTGGCTGTGGCGCGTGCCGAGCTTTGTGTGCAGCCCCGTGTGTGTGCAGAGTGGAACTGGAAGCAGGCCTGTGTGCACCTTCCCATCACCATCCCTGCCCCCTGCTGCGCCTTCTTCCTGCCTCTTGCCTGTCTCTTCTCCCTCCCTTAACCTCGTGAGCTTGTCCTGGTCCCAGTGCCTCTACCAGCCTGCCTCCTAGCATCTGCAGGGATGGGCTGGGAGGTCTGGGGGGCTTTGTGAATTCCACGTGGTCCAGGCTAGACCCCTCAACTCCCAGCTCCCCACAGAGATGTGTGGGGCTGGGGGCTCTGCTGAGGGGCAGGGAAAAGGCCCTGCTCTATTAGTTTGTCCCAAGGACCACAGGTAGGGCGCAAAACCCAGCAGCACAATAACCTCAGAGCCCTCGGGCCTGGCAGGACCTGACGGCAAAGGGCAGGACCCCAGGCCCTTGGCCAGTCCCCCTGCCCTGGTCAGGTCGGCAGCCCTTCTGTGGCCTGAGACTGGCAGCCACAGCTCAGAGAGGTGTGCCTCTGTGGCCCACTGGGGGGCCCTGGGCAGAGTCTTCCTGAACCAGTTGGCATGGAGGGGCTGAAGCCCCCATAAGCCCACCTCATGCCCCTCTCATGGTCCTCAAACCAGAGTCCTCTGAGACCTGTGATGTCCAGGTCTTATCTGAGACCTGGACCAGGAAGCAACTTCTTGGGAACCCACAGCATGGCCGTGCCCTGGGACACCTGGCCAGATGGAGTTAAAACCCAGTGAGATCTGGGAAGGGAAGCAGGGTGGCTTCAGGGTTCCCCTGGGGGCTCACTGTCACCCTGGGAGCCTGGTGGACCTCACCTTCCCTGGCTGTGGGACAGCCTAGACGACGCTGCGCCCCTCTCTGCCCTGCAG
Seq C2 exon
GATTACGTCTTCTACCTGGAGCCTGAGAAGCTCGAGTCAGGGAAGGGCAAGTGTCCCTACGACCCCAAGCTGGACACAGCCTCAGCCCTCATCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000018307:ENSBTAT00000024362:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.290 A=NA C2=0.062
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(6.3=100)
A:
NA
C2:
PF0140314=Sema=FE(6.6=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:
CCACTCCCTGGACCCAGATG
R:
GATGAGGGCTGAGGCTGTGTC
Band lengths:
185-1818
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]