BtaINT0130821 @ bosTau6
Intron Retention
Gene
ENSBTAG00000021920 | SEMA4C
Description
sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4C [Source:HGNC Symbol;Acc:HGNC:10731]
Coordinates
chr11:2786107-2787343:-
Coord C1 exon
chr11:2787231-2787343
Coord A exon
chr11:2786265-2787230
Coord C2 exon
chr11:2786107-2786264
Length
966 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGCC
5' ss Score
7.58
3' ss Seq
CTCCTGTGCTTCTCTGGCAGAAG
3' ss Score
7.96
Exon sequences
Seq C1 exon
GAGACGGCTGGCTTCTCAAGGCCGTGAGCCTGGGGCCCTGGGTTCACCTGATTGAGGAGCTGCAGCTGTTTGACCAGGAGCCTGTGGAGAGCCTGGTCCTGTCCCGGAGCAAG
Seq A exon
GTAGCCATCAGGCCCCACCCACCGTGTCCCCGCATGGCCCCCAGTCGTGTGCCTGGCCAGTCCAGGGGCGGGGAGATGCCCAAGAGGGAAGCGAGAACGCTCGTGGAATCTGCACTCTGCGGGCGCCCTATCTTCTATACAGCCTGGTCCTGACGGCGCTTGTCAGCTGTTTTTGGGCCCCTTGAGGGGACTGTGCCGCCGCCCACCCGGCCTTGTGCCACTGTGGCTCCTGACGCCCGTGTGATGCCTCCTTGCCTGCCAGCCCCGGCCCCCAGCGTAGTCAGCAGTTCCCTGAAGTGCCACTCGAAGCTTCCCTCCCCCATCCACTCTCTTCCCGCGTGTCTGTGGCACTTTCACATGCTTGGCTTTTCCCAACTCTGGAGGCTCGGGTTGTTCCCCAGAACGTGGAACCATGGCAGAAAGAAAGCCTGTAGTTGCAGAAACACACAGATTGGCGATCTCCATTGAAACAGAGGAAAATGCCTTCTGCTTTGCTGGTGCTATTGTGAGGCTGACGGGATCTGCGGAAACTGAACTTCCTGCTCTATTTATACTACTCTGGAGCCGTGCGTGTGTGAGAGAGAGAGAGTGTATGTGAGAGTGAGTGTGTGTGAGTGTAAGAGTATGTGTGTGCGCTTGTGTGTGGGGGGACTGTGAGTGTGTGTGAGTGGGTTTGTGTGAGTGTGAGAATGTGTGTACATGGGTGTGAGTGAGCAGGCACAAGGATACTTCTCAGCCTCCCAGGTCTGCTGTTTGTTTCTAACAAGGTCACGGCTGTAAGGGGCTTAGGATTGCTCCTGGCTTATAGTAAGCCCTCCGTGCCTTCCCAGCCCTCAGATTTCCCGCTTTGGGACGCGAGCACAGCCCACTTCCTGCTTTGGGCCCCGGCGCCCTGGCAGTCATCCGAGCCCCCGCCTGGGCCGTGTCCGGACCTGGCTCAGTCTCCCTCCTGTGCTTCTCTGGCAG
Seq C2 exon
AAGCTGCTCTTCGCGGGCTCCCGCTCCCAGCTGGTGCAGCTGCCCCCAGCCGACTGCATGAAGTACCGCTCCTGTGCCGACTGTGTGCTCGCCCGGGACCCCTACTGTGCCTGGAACGCCAACAGCAGCCGCTGCGTGGCTGTGGGCGGTCACTCCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021920:ENSBTAT00000029225:12
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=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(8.6=100)
A:
NA
C2:
PF0143720=PSI=PU(60.3=66.0)
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:
GAGACGGCTGGCTTCTCAAG
R:
CTGCTGTTGGCGTTCCAGG
Band lengths:
241-1207
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development