BtaINT0130824 @ 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
chr11:2789744-2791472:-
Coord C1 exon
chr11:2791324-2791472
Coord A exon
chr11:2789893-2791323
Coord C2 exon
chr11:2789744-2789892
Length
1431 bp
Sequences
Splice sites
5' ss Seq
GGGGTGAGT
5' ss Score
7.93
3' ss Seq
CTCCGGCCTTGTTCCTGCAGAGC
3' ss Score
11.05
Exon sequences
Seq C1 exon
CAGGGCAGCTGGCCTGGAGCTCGGCGCCCGGGCGTGTGCCATGGCCCCACACTGGGCCGTCTGGCTGCTGGTACTGGAGCTGTGGGGCCTGGGCCTTGGGGCTGAGGTGTGGTGGAACCTGGTACCCCGGAAGACGGTATCTTCTGGGG
Seq A exon
GTGAGTGTCTGAAGGCTGGGGAGCAGAAGGCCAGGAGGGACTGCTGGGGGAAGATGGGTGCTAAGTAATTGCCTTCTGGAACGTCTGGCTTCATTCTGCAGTTGGGCTCAAGGCCCTCATGTACGTGACACAGCTTTCTAAGAAATATGAGTGGCTCTAGGAACCCAGAACTGGTCGTCTAGGCCAGGATCCGGGGTGGCCCTCCTTACGCTTAGGACCTGGCTGCCTTGTTATCCAAGAGTGATCATTCTTCACCTCTCTCCCCACATCTCACTTCTGGAATTATCCCTAGCACTGAGAGCCTAAAGAGAGAAACCTGAGCCGAGATAAGCACGAAGCAAAGGGTGTTACTGCCCACTCCCAAGTCTTCAAGCTCTGTGCCCCCAGGAGCCCCCTTAGCAACCCTGATATGATAGACTCCCCCTTCTGCTGACCTGATACGCGTGCCATCTGATGGCCCTGGGTGGGGTGTGTGTGTGCACATGCTCCTGTGGGGGAGGGGGTCAGTGGGCCTGACAGCCCTTCTGTGCACACACACCTGGATGCAGAGGTGATGTCAGGTGTTTGTATCATCCGTGCGCTCTGGGGACCTGGGATGAGCTCACCTCCCACAGGCTCCTCGGTGCTAACGACGCCCTCCCTTGCCGGTCTGTGTCTGGGCCCATCGTTGGCTCCAAACACTAAGGGTGGTTTAGGGGGACCCTGAGGACAGTCCAGCAGCTGTTTTGGGGGTTGACGTGGGAATCCTGTGGCTACATGAATGTCGTGGCACCCTGCTCGACGGATGGCAACAGGTCTCCCCAGCCCCAGGCTGCAGCACTATCCTGGTCCCCAGCCTCTGGTTTCCCCCGCCCTCCCTGCCCTGGTCTCCCAGCCCGATTCCGTCTCCACATCCCATGGCCGGCTCTGCTCGTACCCTTAGCAGCCTGCATTTGGGACCCACAGGAGGGAAGGTTCTCTAAGACAAGGAACGCTCTCAACTTCCGTCCATCCTGCCCAGCTGGATCAGGAGCCAGGGCAAGGCTGGACCCTGGTGGGGGCAGTGGGCAACAGAGCAGAGAAGGAAGTGGGGGCGGGATGGGGAGGTGGCTACTGACCCTGAGAGTGAGAGCCATCAGTCTGATGGCTTCCTCTGGCCGGAAGCTGTGGCTGAGATATCCTTCCTTCCTCCTCTCCAGCCCAGATTTGCCTCCCTGGGTGGGGAAAGCCAGGGAGCCCTGGGTGGAGCTGTCAGAGTCAAAAGCCTATTCAGAAAATGCCCTTTATTGCTGGTCAGAGGAGCTTGGCTGGCATCTGCTTGTGGGGTGCTGGCTCTAATGTGCGGTGACCACACTGGTCAGAGGAGGGCTAATTCTGGGGGAGAGGGGATGCCTGGAGTCCCGGGAAGGTCCACTCACCCCAGCCCTGGTCACTCCGGCCTTGTTCCTGCAG
Seq C2 exon
AGCTGGCCACGGTGGTGCGGCGCTTCTCCCAGACGGGCATCCAGGACTTCCTGACGCTGACCCTGACTGAGCAGACGGGGCTCCTGTACGTCGGGGCCCGGGAGGCCCTGTTTGCCTTCAGCGTGGAGGCTCTGGAGCTGCAGGGAGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021920:ENSBTAT00000029225:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0140314=Sema=PU(7.7=66.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGCTGGCCTGGAGCTCG
R:
ACTCCCTGCAGCTCCAGAG
Band lengths:
292-1723
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development