BtaINT0130799 @ 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
chr3:14675086-14675513:-
Coord C1 exon
chr3:14675415-14675513
Coord A exon
chr3:14675192-14675414
Coord C2 exon
chr3:14675086-14675191
Length
223 bp
Sequences
Splice sites
5' ss Seq
ATTGTGAGT
5' ss Score
7.35
3' ss Seq
AGCCACTTCCCCCCCTCTAGGAA
3' ss Score
8.58
Exon sequences
Seq C1 exon
ACACAGTGTTTCAACTTTATTCGTGTCCTGGTATCCTTCAACTCCACCCACCTCTACGCCTGCGGCACGTTTGCCTTCAGCCCTGCTTGTACCTTCATT
Seq A exon
GTGAGTTATCTGGCGCCGGCTCTCAGGCCCCGCCTCACCTCCACCCCAGCTCATCCTCTGCAGCTCTGAAAAACTCTGATGTTGCGGCCCAGGGTCCTTGTGAGCTTCCGAGCTCCAGGTCAATTTTCCTCTGCACCCCCTACCCCTTCCTCCCTCGTGTCCCTCCTTTCCCAGACGTGAGACTCTGGCGTTCTGGCCCCCCCAGCCACTTCCCCCCCTCTAG
Seq C2 exon
GAACTCCAAGATTCCAGACTGTTGCCCATCTCGGAGGACAGGGTTGTGGAGGGGAAAGGCCAAAGCCCCTTCGACCCCACCCATAAGCACACGGCTGTCATGGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000012228:ENSBTAT00000016223:4
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=0.167
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(7.7=100)
A:
NA
C2:
PF0140314=Sema=FE(10.2=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:
ACACAGTGTTTCAACTTTATTCGTGT
R:
CTGCCATGACAGCCGTGTG
Band lengths:
205-428
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]