BtaINT0130945 @ bosTau6
Intron Retention
Gene
ENSBTAG00000007281 | SEMA6C
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C [Source:HGNC Symbol;Acc:HGNC:10740]
Coordinates
chr3:19724875-19725464:+
Coord C1 exon
chr3:19724875-19725048
Coord A exon
chr3:19725049-19725317
Coord C2 exon
chr3:19725318-19725464
Length
269 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGC
5' ss Score
8.69
3' ss Seq
TCCCTCTGGCCTCACCTTAGGTG
3' ss Score
8.96
Exon sequences
Seq C1 exon
GGCCCTACTGACCCAGGTGGCTGTGGATGGCATGGCTGGTCCCTACAGTAACATCACAGTCCTGTTCCTTGGCTCCAATGATGGGACAGTGCTGAAGGTGCTGCCCCCAGGGGGGCAATCTGGGGGCTCTGAGCCCATTCTGTTGGAAGAGATCGATGCCTACAGCCCCTCCCG
Seq A exon
GTGAGCCCTTTGTCCAGCAGGCCCCCTGCAGAACAGGGATGGAATGTGAGGTGGGAGATGGGGATATGGGGATGGGGGGGGGACTCCGATATTGGAAGTTGTGGGGAAGAGAGAGGGACTTGGAGAGATGACATTGTGTAGCACGGCAGGGTAGCCCCATGAGTTGTATTCAGTTGCTTGTATGCCTCCCCACCTTCTTTTCTTTACCTTACCCAGGGAAAAAGGAGCCTCACCTGCTCCACCTCTGACTCCCTCTGGCCTCACCTTAG
Seq C2 exon
GTGCAGTGGGAAGCGGGCAGCCCAAACAGCACGGCGGGTCATAGGGCTGGAGCTGGACACTGAAGGTCACAGGCTCTTTGTGGCTTTTTCTGGCTGCATCATCTACCTCCCTCTTAGTCGGTGTGCCCAGCATGGGGCCTGTCGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000007281:ENSBTAT00000009575:13
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.102 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(13.7=100)
A:
NA
C2:
PF0140314=Sema=PD(2.1=18.0),PF0143720=PSI=PU(14.5=18.0)
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:
CTACTGACCCAGGTGGCTGT
R:
CACACCGACTAAGAGGGAGGT
Band lengths:
295-564
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]