BtaINT0130946 @ bosTau6
Intron Retention
Gene
ENSBTAG00000007281 | SEMA6C
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C [Source:HGNC Symbol;Acc:HGNC:10740]
Coordinates
chr3:19725318-19725815:+
Coord C1 exon
chr3:19725318-19725464
Coord A exon
chr3:19725465-19725737
Coord C2 exon
chr3:19725738-19725815
Length
273 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGA
5' ss Score
7.66
3' ss Seq
TATGACTCAGTTTTCCCTAGGAG
3' ss Score
4.34
Exon sequences
Seq C1 exon
GTGCAGTGGGAAGCGGGCAGCCCAAACAGCACGGCGGGTCATAGGGCTGGAGCTGGACACTGAAGGTCACAGGCTCTTTGTGGCTTTTTCTGGCTGCATCATCTACCTCCCTCTTAGTCGGTGTGCCCAGCATGGGGCCTGTCGGAG
Seq A exon
GTGAGAGGGCCTTGAGGCCAGGCTCCCTGGGCCTGCAGGCACAAAGGCATTGGGGGTGGCAGGGAAATGCAGGGGATGGTTGTGTGTGGTGGGATGTCCACAAGCATCCTGCCGGTGGGCAGTCACCAGGGACAGGACTAGGGATTGGTGTGGATAGGATGGGAGTATCAGGCTAGGAGCCTCCTGCAGGCCAGGGTGAGAGTGAAAGAGGCAGGGGAATGGACTGTAATTAGAGTGGAGGGTCCCAGCCTCATATGACTCAGTTTTCCCTAG
Seq C2 exon
GAGCTGTCTGGCTTCTCAGGACCCATACTGTGGATGGGACAGCTCCAGAGGCTGCGTGGATATCAGGGCACCTGGTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000007281:ENSBTAT00000009575:14
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=0.148
Domain overlap (PFAM):
C1:
PF0140314=Sema=PD(2.1=18.0),PF0143720=PSI=PU(14.5=18.0)
A:
NA
C2:
PF0143720=PSI=FE(41.9=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:
GGGCAGCCCAAACAGCAC
R:
GTGCCCTGATATCCACGCAG
Band lengths:
204-477
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]