BtaINT0130968 @ bosTau6
Intron Retention
Gene
ENSBTAG00000016800 | SEMA6D
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D [Source:HGNC Symbol;Acc:HGNC:16770]
Coordinates
chr10:62869126-62870826:-
Coord C1 exon
chr10:62870770-62870826
Coord A exon
chr10:62869294-62870769
Coord C2 exon
chr10:62869126-62869293
Length
1476 bp
Sequences
Splice sites
5' ss Seq
CTGGTTAGT
5' ss Score
6.32
3' ss Seq
AAATCTGTTTGCCACCACAGACA
3' ss Score
5.36
Exon sequences
Seq C1 exon
AAATTTTGCCTACTTCAACTACACCAGATTACAAAATATTTGGCGGTCCAACATCTG
Seq A exon
GTTAGTTTTTTTTCATTTTTTTGAATTAACAAACCTTTTCTTTCCTTCAGTTCAGCATTTTCAGCCCCTTCTCCCCTCCTTTTGCGCAGTTTGGCAGCCCGTCATTTTTGTGCTTTGACTCATAACCCCCGATGGTCCCAAAGACTTTTTCTTACTCAGCACTTCACCTTGTGTAGCATGTTAATAGTCCATCATTGACCAAGGCGCACATCCTTAAGAAAAATCCAATGGATTAACATAGGCTGCATTCCAGCTGCACGCCCGTCCACCTGAGCTTTCTTCTCTCACCCCTGCGCATCGTGAATGTTCCCTGCAGCCATCTATTTTTAATGGATGGCAGAACTTCATTATTTCCCCCTTCTCTCCTCACCTTTCCTAAGACCTAGTAAACAAATACACATTTCCCCAAAATGTGTATTTATCAATTTTAGAGATCTTTTTTGGAATGGTTTGTGGTAATCTCTGGAACCTTTGAATGCTGTGATCTCAGTGGTATGAAGAAGGTCCCCATCGAATGAAGCTGGTTTCTGATGTATTAAGATGTCCACTGGGTTCCCTGTGCCTCCCCGCCCCTGCCTTGTCTTCATCTGTTCTGGAGTCTTCATCTGTGACCGTTGTACCAGTCTGAATTTGGGTCTCCGGAGTTTTCGCCTAAAATCATACACTTCCATTTTGATGGAAAATCTGCTTGGCAGAACTCAGTAATAGACGCGCTAAGAGGTTAAGTTACTCCCGATCCTGTCGCTGGTTCTAAAATTCACTAGCTGTTTCATTCCTCAGAGGGGAGAAAAGAATGGTAGATCCTATGTATCAGGACACCCTTAATCAGCTCATAAATGCCATTTCTTATGCATGAGTTGCCTCTTACTCTTTGGGAAAAAAACTCCACGCGCATTCTGGAAAGCTTCAGTGCTTCCCCATGGACAGTGACCCCTCAGTGCGCTCAGGAATCTACAGATGGGCCGGAGGTCTATGCTAAAGCAGGACAGCCTGCTTGTCAAGTCCAAGATCGAGTGTTTATGCAGAACCAACCAGGTGCTTTCTGACGAAGTTACACTCTAGGTTCCCCAGTGAAAGATATACAGCTTCCAACCATCAATCAAAATTATTTTTTAAAAATACACAAAAAGAAATGAAATGATGCTGTCCCACAAAAAGATGAGGAAATCACAGTCTGTGGGATTCATATTACCTTTTCCATGAGTGTCATTAATCACCCCAGAGGTTTCAGTAGGAGTATTTTGAGTGTCTTCAAATTTGAAATCTGCTTAATGTGTCTTTATGATTAATTTTTAGTTTTTCTTTTTCCCTTGCAAGAAAGGGATTTGGTGTAATCTCCTTAGATGTGTTTTGATGAAATCCTCGAACAGGCTTTCTCATAAAATTTGCTTAAACTTTACTTGAAAATACAACAGTCCAGTCAGAAACAATGGGCTGACATTACCCGCGTTAATAAAAATCTGTTTGCCACCACAG
Seq C2 exon
ACATGGAGGTATCTTCATCTTCTGTTACCACAATGGCAAGTATCCCAGAAATTACACCTAAAGTGATTGATACCTGGAGACCTAAACTGACCAGCTCCCGGAAATTTGTAGTTCAAGATGACCCAAACACTTCTGATTTTACTGATCCTTTATCAGGTATCCCAAAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000016800:ENSBTAT00000022349:17
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.100 A=NA C2=0.298
Domain overlap (PFAM):
C1:
PF0143720=PSI=PD(8.1=25.0)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Mouse
(mm10)
No conservation detected
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATTTTGCCTACTTCAACTACACCAGA
R:
AAAGGATCAGTAAAATCAGAAGTGTT
Band lengths:
206-1682
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development