BtaINT0029749 @ bosTau6
Intron Retention
Gene
ENSBTAG00000019513 | C9orf50
Description
chromosome 9 open reading frame 50 [Source:HGNC Symbol;Acc:HGNC:23677]
Coordinates
chr11:100036754-100038242:-
Coord C1 exon
chr11:100037723-100038242
Coord A exon
chr11:100036848-100037722
Coord C2 exon
chr11:100036754-100036847
Length
875 bp
Sequences
Splice sites
5' ss Seq
CGAGTGAGG
5' ss Score
4.44
3' ss Seq
GCCCCCCACCCCCACCCCAGCAC
3' ss Score
5.22
Exon sequences
Seq C1 exon
ATGCCCCGGCGTCGCCCCAGCTTCTGGGCCCAGCAGGTGGCGCCCGAGGGACTCCCCGGCGGTGGCGATCGCCGGCGCAGAGACCCGCTGCTGCCCAGGCTGCTGCGGCCCGAGCTCCGAGCAGCCTCGGACGCGGGGGTCTTCGGGGTCTCGAGGGCCTCTGAGAGCGGCGCCGAGCGGTGGCAGGCCCCCCAGTGTGAGTCCTTGCACTCCGATCCCGGGCTGGGCTTCAGGCGCTCCCGGTCCCGCCTGCCGGTCCTGCCCACCGTGGCCCAGCGGCCGGCGAGGAGCCGGACAGTGCTGAGGTCGCTGCTGCTGCCGCCCCTGCTCTTGGCCGGCGAGCCCCCCGAATCGGCGCCCGCATGCCCCGAGCTCGGACAGCGCAAGGACCCTCGCAGGGGCTCGGCCAAGGAGACCTCCGATTCCTTGGGCTCCCTCCTAGGAGAAGTTCTTCCGGGCCGGTTCCGGCAGTTCCTGCGACAGTTCAGGGCTGACTCTGCGGAACGGCTTCTCCCACCGA
Seq A exon
GTGAGGCCCCTGTGGCTCCCCCCCAGGGGGCGGGGCAAGGCGGGGCTGCGTCATTTCCGGTGGTGAGGGTGGTCGGAGTGGGGGTGGTTGGGTGGGGGGGTCACACCACCTGGCACAGAAGGATGCTTGTATTAGTGAAGTAGGGCTGGCAGAATCCTGACAACCACTGCTTGAGGGCGGCCCTGCCATTGTACAGATGAATAAATAGCATCACATTCCACAGAATGAGAGCTCAGTCCCACAAGTCTGCCCCCACCCTACTTCAGACCACAATTGCCAAGTCCCAGGTTGTCAGTGTGATTCTGACCTAACAGCTATAAACCTGAGATTCCCAAGACCTCTTTCTTGGGTTTGTTTGGATTTGTTTGTTAGAGCAGCTCACAGAGTTCAGGGGAAACACCTAGGCTACAAGTTTATTGAAGGATATGATAAAGGATGGGCTCCCCCAGTGGCCCAGGAATAAAGAATCTGCTGCAACGCAGGAGCCGCAGAGATGCAAGATTGATCCCTGGGTTGGGAAGATCCCCTGAAAGAGGGCACGGCAGTGCTTTTGCCTGGAGAATCCCATGGACAGAGGAACCTGGCAGGCTATAGTCCAGAGGGTCACAAAAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTGGCAGAATCCTGACAACCACTGCTTGAGGGCGGCCCTGCCATTGTACAGATGAATAAACTGAGGCCCAAGGCCATGCAACCAGGAAGACTCTAATAAAGACTGTCCCCAAGCGAAGGCTCATAACTCTTTCTACTTCATCCTGCCCCCCACCCCCACCCCAG
Seq C2 exon
CACCCTCAGCATCTCAACATCAAAGGCATTCTGCGTCAGAGTTCAACGGAAGTCCTCCTCGGTGTTCCAGCTCCCACTTCCTCCCAGAGCTTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000019513:ENSBTAT00000025995:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.655 A=NA C2=0.645
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Rat
(rn6)
No conservation detected
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:
CAGTGTGAGTCCTTGCACTCC
R:
TGATGTTGAGATGCTGAGGGTG
Band lengths:
350-1225
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development