BtaINT0108834 @ bosTau6
Intron Retention
Gene
ENSBTAG00000004176 | PDC
Description
Bos taurus phosducin (PDC), mRNA. [Source:RefSeq mRNA;Acc:NM_001166527]
Coordinates
chr16:69012513-69013701:-
Coord C1 exon
chr16:69013641-69013701
Coord A exon
chr16:69012665-69013640
Coord C2 exon
chr16:69012513-69012664
Length
976 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGC
5' ss Score
9.88
3' ss Seq
TGCTTTAAATTTTATTCCAGGAC
3' ss Score
8.48
Exon sequences
Seq C1 exon
ATGGAAAAAGCAAAAAGCAAAAGTTTGGAGGAAGACTTTGAAGGACAGGCCTCACATACAG
Seq A exon
GTAAGCAAAGTCAGAAGAAAAAAACAATTGTAGACTTAAAATTAAATTTGGAGATCTCTTATTGTCATTACTCAGTATGAAACTTAAGTAATACCTTTGAATGGGTTGATGGAATCATCTAAAAAATATTTGACTGCATAAATTAATGTGAAATCGAATACTTTTGAAACAATTTTAATTAGATATCAAAGAAAGAGAAAAACACTGATTATTGAGAATTTCTTGCTGTCTGTCATAAAACCTCTCTATCTACACTACACGTAAGCCACTTTTCTTCTCTCCTAATTTCTCCCACTATGGGCTTTCTTTGCCATTGTAAACAATAGAAAACCAAAAGAAAAATAAATAAATTGAGTTTTCAATTTTAATTTTTTGAATCTAAAAAATACAATAATTTTTAAAAATATAAATTTGTTTTAATTGGAGGCTAATTACTTTACAATATTGTATTGGTTTTGCCATATATCAACATGAATCTGCCACGGGTGTACACGTGTTCCCCATCCTGAACCCCCTGCCCACCTCCCTCCCCGTAAAAATTGATTTCAAGATTCTTCCAGAATAACTAAGACTTCATTTTATCCAAAGCCTGTTTTCTTGATCTGTTAAATTGTGTGTGGCTGTCTATATACCACTAGCAAGAGTTTAAAAGTCAAATAGCATGGTTTAAATTTTTAAATTCAAGTTTCTTTTAACTCTTTTGAATCTTATTTAAGTAATACTCCCTTCTCTGTTTAATAATCATACACAATTTTTAGATTTAGTCAGGAGTTTGAATGAATTTATATGAATACTAAACAAAAATCCATGAAAACTAATTTCATAATGACAGTGACCTTCTAAGTATAACACAAAACCAAGAAATCACAAAGGAAGATTGATAAATTTAGCTATATAAATGAGGAAAGGAAGGAAGGAAGAGAGAAAGGGAAGAAACATGGAAAGGGGAGACAGTTTGCTTTAAATTTTATTCCAG
Seq C2 exon
GACCCAAAGGAGTAATAAATGACTGGAGAAAGTTTAAATTGGAGAGTGAAGATAGTGATTCAGTTGCACCCAGCAAGAAGGAGATTCTCAGACAAATGTCTTCTCCTCAGAGTAGAGATGACAAAGACTCAAAAGAAAGATTCAGCAGAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000004176:ENSBTAT00000005468:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.549
Domain overlap (PFAM):
C1:
PF0211411=Phosducin=PU(8.2=95.2)
A:
NA
C2:
PF0211411=Phosducin=FE(20.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCAAAAAGCAAAAGTTTGGAGGA
R:
TCTGCTGAATCTTTCTTTTGAGTCT
Band lengths:
201-1177
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development