BtaINT0130941 @ bosTau6
Intron Retention
Gene
ENSBTAG00000007281 | SEMA6C
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C [Source:HGNC Symbol;Acc:HGNC:10740]
Coordinates
chr3:19717720-19719651:+
Coord C1 exon
chr3:19717720-19717739
Coord A exon
chr3:19717740-19719482
Coord C2 exon
chr3:19719483-19719651
Length
1743 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGG
5' ss Score
11.08
3' ss Seq
ACTTCTGTCTTCTCTTTCAGGGC
3' ss Score
14.39
Exon sequences
Seq C1 exon
CACAGGAGTCACCACCCCAG
Seq A exon
GTAAGGAAAGGGCAATAGCCCCTGAGGGCAGGGGATGGAAGTAGGCATGGCCTGGGAACAGAAGAGGGTCAGATCATTCTCCCCACTTGCCTGAGACTGAAGTTGTTTCCTGGGTGAAGATACCAGTTGCCCAGGGCAACTTGGGGTGGGGGGGGCAGGAGGGGGAGGATAGGAGACAAGCTGTGTCCCTTTCTCTTCCCCTAGGAGCAGCACCATCCGGAACCATTGTGGGGTGGGGGGCGGGGAGGGGATGGTGGCAGAGGGAGGCTTGGCCTTTCAGCACCAGAGGGTCGTTAGCTAGCTGACTGCTCTGCCCCTGGGGAGGGGGTCATCATTAGGTGCTCCTATCCCTTCCCCTCCTCCAGCTCTCTTGGGATCCCATCTGACGTCAGCCTCCCCATTAATGACGCTGGATTGGGGGTGGGGTACACTTGGGTCCTGGCTCCAAGAGTGGAGTTGTGGGGGAGATGGAATGGGGGAGGCCTGGAAGCCCAGGGTCTCTTCTTCAGGGAACATGGCAGGACAGGCAACTGAGGATTAGTGTAGGATAACTGTCTGTTCATGGAAAGGAGGGAGTCTCACCCTTGCTGACCTGATTTCCTGGGCTTACTCAGCCCCTCACTTCAATATCAGGGGAAGGCAGGAAGCTGGTGTCCACCTCCCACTGTGGGTTCTAGCCAGGGTCAGCTTGGCTGGTGAAGGCCGATGGAGGCTGATGGGTGGGAAGGAGGGCTGTCTTACAGTCCCTTCCACCATATCTTTCTTTTCCTGGACTTTGGGCTATAATCGCCTGCCTGTCATTGAATTATTTACATTTTCATTCCACGGCAGCCCAAAGAGGGAAGGAAGGGAGAGAGGGACATATTCAGTCATATCTCCTCACCAGTATAGCCTCTTCTATGACTGGCTCCTCACAGGGGGTGGGTCTGCTCTTTTACAAATTGAGCACATGCAAGGTTTCTTAGGAGTTGGGGAGGGAACAGGGGGCTAGGGAGGCTGGGAGGGGGCACAGTGGTCGGGCAGACAGCTGCAGCCAGAGCTAAATTTAGCCTCTGATCTGGCTTTGATGCAGATTCATTTTTGGCTAAGACAGCCCCCCTCCCTCACTCCCCTCCCTACGCAGCTTCCCCCTAGCAATGGAAAGGGCCCTAGAAGCAGGAGCTTAGACCAGGGCAAAGACCCCTGGGCTGCCTCCCCAACTCTGTTCTTCCTGAGCCGTAAACAGGATGATGGCTGCCTCACAGCTGCCTCTACCAAGGCGCGGTGCCTAAGTTGCTCCCAGGGTGCCATGGAGGTCTGTGAGGGAGGGGAGGCAGACATGATATCCTCTTCCTCCCCCCCAGTGCCAAGGAATCACTATTTATAATTTTAAGGCTTCAGTGTCTAATTATAGCTGAGACGAGGTTAGCAAGAGGGGGCCAGGAGGTGTCACCTACCGAATGTCCCAGGCCGAGTCAGGAGAGAGGAGGAAAGGCTGAGTGAGAAGGCTGGGGGGAGGGAGCGGGCGTATCCTGTCCTTACCTGGGGTCACACTGGCAGGCTTCACACCAGCCAGTTGGGGCCAGTTGGAGAGGGAAGGGCCTTGAGTGACAGTGACAGCCGGCTGGCACTGAGGCAGTGCCAGAGATAGGATTCTTTACCCTTCTCCGCAGGGTCTTCTGGGGATAGACCTGGGAAGGAGCCCTCCTGCTTCAAAGGTGGAGGACGTTTGGCCCCTTCGCCCACTTCTGTCTTCTCTTTCAG
Seq C2 exon
GGCCAGCATATGGGTGAGGGGGCAGCCCCTGGGGCCTGAGCTGCCCCACACAGAATGCCCCGTGCCCCCCACTTCATGCCCTTGCTGCTACTACTCTTGCTCTCAATTCCACACACGCAGGCTGCATTTCCCCAGGACCCTCTCCCTCTGCTGACCTCTGACCTGCACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000007281:ENSBTAT00000009575:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.000
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
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:
CACAGGAGTCACCACCCCAG
R:
GTCAGAGGTCAGCAGAGGGAG
Band lengths:
182-1925
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]