BtaINT0130950 @ bosTau6
Intron Retention
Gene
ENSBTAG00000007281 | SEMA6C
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C [Source:HGNC Symbol;Acc:HGNC:10740]
Coordinates
chr3:19726560-19728079:+
Coord C1 exon
chr3:19726560-19726655
Coord A exon
chr3:19726656-19727090
Coord C2 exon
chr3:19727091-19728079
Length
435 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGG
5' ss Score
9.16
3' ss Seq
CTTCTCTCTTCGGTTGGCAGGCG
3' ss Score
7.95
Exon sequences
Seq C1 exon
TGCTTCTGAGTCCTGGCCCTTCCCCTGAGACCCCCAGTCCCCCCAGTGATGCCCACCCCCGGCCCCAGTCTTCCACTCTTGGAGCTCACACTCAGG
Seq A exon
GTAAGGGGGCTGGTTGGGAGGGACAGGAGTGAAGTGTGGAGCTGCCAATTCTTGAAGAATTCTAAGCCCCTCACTGATCATTGTTTGGTGTTCACTAATAATGCCTGTTTGGAGCCTCCCCTCCCTTCCCCTCCCCAGAGCTGGCCCTCCCAGCCCCGCCTCCTTCAGCACGGGCAGAGTTTGGCAGTTGCTCTTGGCATGGCTACAGAGGCCTGAGCTGGGATGGAACTCCCCAGGCCCAGGCTCTAGCTTGTGTGTGAGGGTGGTTGGGTGGGCTGTGTGTTGAGGGGTCAGGGGAGGAGACTCCTGAAGAGGGTCAAGGCTGTGTCGGAGTGAAAGCAGAGCAGCAGTGGGAGAGAGGGACACTTCGGAACTCGCCTTCCCGCTGGCCTACCTTCGCTGAGCCTCCATCTCTCTTCTCTCTTCGGTTGGCAG
Seq C2 exon
GCGTGCGGCGGGACCTCCCTCCAGCCTCAGCCTCCCGCTCAGTCCCCATCCCACTCCTTCTGGCCTGTGTGGCTGCGGCCTTCGCTCTGGGCGCCTCGGTCTCTGGCCTCCTGGTCTCCTGCGCCTGTCGCCGAGCGCACCGACGGCGGAGCAAGGATATCGAGTCTGCAGGGATCCCACGTCCTCTCTCCCTCCGCAGCTTGGCCCGGCTGCATGGGGCGGGCCCAGAGCCGCCGCCGCCGTCCAAGGACGGAGAGGGGGCCCAGACGCCGCAGCTCTACACCACCTTCCTGCCTCCCCCCGAGGGCGTACCCCCGCCGGAGCTGGCCTGCCTGCCCACCCCGGAGTCCACGCCAGAGCTGCCGGTCAAGCACCTCCGCCATGCTGGAGGTCCCTGGGAGTGGAACCAGAACGGGAATAACGCCAAGGAGGGCCGGAGCCGCGCCCGGGGCGGGAACGCGGCGGGTGGCGCCGCGCCGCGCGTGCTGGTGAAGCCGCCGCCGCCTGGCTGTCCCGGGCAGGCCGTGGAAGTCACCACCTTGGAGGAACTACTGCGCTACCTGCACGGCCCGCAGGCGCCCAGGAAGGAGGCCGAGCCCCCGGTCGCCGCCCCTTTCACCTCGCGGCCGCTGCCGCCCGAGCCCTCCCCCACCCTCTTTGCCGGCCCCAGCCTGCTGCCCCGGGACTGTGCCCCGCCTCGGAGGCTGGACGTGCCCCCGGAGGGCAAGTGCCCGGCCCCGGCCGCCCGGCCTGCGCTCTCCGCCCCAGCTCCCCGGCTCGGGGTGGGCGGCAGCCGGAAGTTGCCCTTCTCCTCGCACCGTGCACCCCCTGCGCTGCTCACCCGAGTCCCCTCGGGAGGCCCCTCCAGGTACTCGGGGGGTGCCGGGAGACACCTCCTGTACCTGGGTCGGCCTGAGGGGCACCGGGGCCGCGCCCTCAAGAGGGTGGAAGGTCGAGAAGCCCCAGGGGCCCCTGAAGCCTCCCTTTGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000007281:ENSBTAT00000009575:18
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.882
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTTCTGAGTCCTGGCCCTTCC
R:
CCCCTCTCCGTCCTTGGAC
Band lengths:
354-789
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]