BtaINT0130773 @ 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
chr22:50737983-50738464:-
Coord C1 exon
chr22:50738345-50738464
Coord A exon
chr22:50738123-50738344
Coord C2 exon
chr22:50737983-50738122
Length
222 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGA
5' ss Score
7.23
3' ss Seq
TGACTCCTGCCCGCCCGCAGACC
3' ss Score
11.11
Exon sequences
Seq C1 exon
ATGAGGAGCTCTATGCAGGCGTGTACATCGACTTCATGGGCACGGACGCAGCCATCTTCCGCACCCTTGGCAAGCAGACGGCCATGCGCACGGATCAGTACAACTCTCGGTGGCTCAATG
Seq A exon
GTGAGAACAGCCTGCAACAGCTCTAGCGGGCAGCATGTCTGGGGTGCTGCACGGAGACCCTAAGGCAACACTCATGGAAAATCTGGGGGCCCTTGACTGGCTAGGGCAAGGGTGGTTTCTTATCCCGGGTTAAGGGAAGAGTTGGGGGTGTTCCTGCACCTGACCTGGGCAAGAAACCTTGTCTGAGGAGGGCCCTGCCTGCTGACTCCTGCCCGCCCGCAG
Seq C2 exon
ACCCTTCTTTCATCCACGCCGAGCTCATCCCTGACAGTGCCGAGCGCAACGACGACAAGCTCTACTTCTTCTTCCGTGAGCGGTCCATAGAGGCGCCGCAGAGCCCTGCCGTGTACGCCCGCATTGGGCGGATCTGCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000018307:ENSBTAT00000024362:7
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(8.5=100)
A:
NA
C2:
PF0140314=Sema=FE(9.7=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:
ATGAGGAGCTCTATGCAGGCG
R:
CAGGCAGATCCGCCCAATG
Band lengths:
260-482
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]