BtaINT0130794 @ bosTau6
Intron Retention
Gene
ENSBTAG00000012228 | SEMA4A
Description
sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4A [Source:HGNC Symbol;Acc:HGNC:10729]
Coordinates
chr3:14663115-14663500:-
Coord C1 exon
chr3:14663382-14663500
Coord A exon
chr3:14663273-14663381
Coord C2 exon
chr3:14663115-14663272
Length
109 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGA
5' ss Score
6.71
3' ss Seq
AGGCTTCATCTCTTTTCCAGGGA
3' ss Score
8.35
Exon sequences
Seq C1 exon
GCACAGGCTCCCTCCACAAGGCTGTGGTGAGTGGGGACCACAGTGCTTATCTGGTGGAGGAGATTCAGCTGTTCCCTGACCCTGAACCTGTTCGAAACCTGCAGCTGGCCCCTACCCAG
Seq A exon
GTGGGAAAGGGCCTGATCCTCAGATGAGGTCTCCAGTGGGGCAGGCCTTGGGTGCTAGGTCCTTACTAGATGTGGCAGGGTGACTTGACAGGCTTCATCTCTTTTCCAG
Seq C2 exon
GGAGCAGTGTTTGTAGGCTTCTCAGGAGGCATCTGGAAGGTTCCTCGAGCCAACTGTAGTGTCTACGAGAGCTGTATGGACTGTGTCCTTGCCCGGGACCCTCACTGTGCCTGGGACCCTGAGTCTCAAACCTGCCGCCTCCTGCCCACCCCCATCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000012228:ENSBTAT00000016223:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.025 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(9.4=100)
A:
NA
C2:
PF0143720=PSI=PU(66.0=66.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACAGGCTCCCTCCACAAGG
R:
TTTGAGACTCAGGGTCCCAGG
Band lengths:
247-356
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]