BtaINT0130952 @ bosTau6
Intron Retention
Gene
ENSBTAG00000007281 | SEMA6C
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C [Source:HGNC Symbol;Acc:HGNC:10740]
Coordinates
chr3:19719483-19721381:+
Coord C1 exon
chr3:19719483-19719651
Coord A exon
chr3:19719652-19721266
Coord C2 exon
chr3:19721267-19721381
Length
1615 bp
Sequences
Splice sites
5' ss Seq
ACGGTGAGT
5' ss Score
11.45
3' ss Seq
CACCTCTCTGTGCCTTCTAGGTA
3' ss Score
10.31
Exon sequences
Seq C1 exon
GGCCAGCATATGGGTGAGGGGGCAGCCCCTGGGGCCTGAGCTGCCCCACACAGAATGCCCCGTGCCCCCCACTTCATGCCCTTGCTGCTACTACTCTTGCTCTCAATTCCACACACGCAGGCTGCATTTCCCCAGGACCCTCTCCCTCTGCTGACCTCTGACCTGCACG
Seq A exon
GTGAGTGCTTGGCACCCTGGCCCTCTATGTGAGCTCAGCACTCAGTCTTGGCAATGAGACACGGAGACCTTTTGTGTGGGTGGCAAGCTGCAGGAGGGCTCTCCGTCTCAAGGAAGCTAAGAGTTGACAGGAAAGGGGAGCAGATAGGTGGAGTGGCACAGAGGCCAGTCACTTCTCATCTGTGGGCCAACTTTCTTCACTTCCAGGCAGCATTGTTCAGTGATAAAGAACAGGGACTCTTGGTCAGACCAAACCGTGGCAGTTTCAAATTCCTGCTGCTCACTTTATAAGGAGTTATTTAACCTTCTTTGCCTCAGTCTCCTCATCGGCAAAATGAAGATAATAATTGTATTCTAGCAGGAATTCCCTGGTGGTCCGTGCTTTCACCACAGTGACCACAGGTTCAATTCCTGCTTTGGGAACCAAGATCCCATGGGCCATGAGGCATGGCCAAAAAATAGTATTTTACCTCATGGAGTTATTTAGGGATTAAATGAGGTAATACAGGTAAAGTGCTAAGAACACTGTCTGGCACAAAGTAAATGATGTATATGTGTTTGCTATTATTATTAGCTACAAAATGAAGGCTTGGGACTAATTCAGTGGTTCCCAACACCTCTTACCTCCCTCTCCACCACTTTATCACCACCACATCTAGGTCCGTCATGGTGGGACTTACTGAATGTCCCAGGCCCAGTCAGGAGAGAGGAGGAAAGGCTGAGTGAGAAGGCTAGGGGGAGGGAGCAGGCTTATCCAGTCCTTACCTGGGGTCACACTGGCAGGCTTCACACCAGCCAGTTGGGCCCAGTTGGAGAGGGAAGGGCCACCGTCCCACCGTGACAGACCTTGCAGATAGATCTATTTGCAGCTTCCTGTTATATATGTAGAATTTAGAGTAATTTTAAGGTTGAAGGAATGGCAGTTAGGTTACTGAGAGTAACTGTTGGGGGATAGATAAGAGTAGCAAACACTTCCATGTGTCAGACAGTGTTCTAATCACGGTACAAATGTTAAATCATCTCTCTCTGAACTCTGGGCTCCCTCTGAACACTGATGACTGTGGTTTCCATGATCAGGCCAGGTGGATGCTGGAGTTGGTTAGAGGAGGCAGAAAGCTTGGAGGATTGAGGTGGTCTGTGAAGAGCCTTGAGGGGAGGGTGCAAAAAGAGGGCTTGGAGAGATGGGGTGAGGAAATGGGACTACGTGGGACAGCATACAATGTGGAAAGAAAGGGAATTGCTAGCCCTAAGGCAGATCTAAGAACTGGGTTGGGCTCAGCTCTGAACTCAGACAGGCCTGGATCTGAATTGGGGTCCCTGCCACTCCCAAGCTAAATGAGCTCTGCAAATTTCTTATTGGCTTTAAGCCTCAGGTTCCTCATCTGTAACATAGCACCAACCTACTTCATAGGGTTGCTGTCTGAAATGAGACAATGCCGCTCAAGTGCTCACACAGTGCTTGGCAGAGGTGAAGTGCTCAGAGTTAGCTGATATTGTATTTAGCCTTCTTAATACCTTTATTAACATGCCCAGGGCTGGGTTTCCTCTGGCTGGGGAGGATGTTGAGGGAGTGTTGTGTCTGAGGGCGTCAGCACCCACCTCTCTGTGCCTTCTAG
Seq C2 exon
GTATCTCTCCATTATCCTGGTTCCGGGGCCTGGAGGATGATGCTGTGGTTGCGGAACTTGGGCTGGACTTTCAGAGATTCCTGACCCTGAACCGGACCTTGTTAGTGGCTGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000007281:ENSBTAT00000009575:2
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(3.3=35.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGCATATGGGTGAGGGGGC
R:
CTGGCAGCCACTAACAAGGTC
Band lengths:
280-1895
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]