BtaINT0108941 @ bosTau6
Intron Retention
Gene
ENSBTAG00000030675 | PDCL
Description
Bos taurus phosducin-like (PDCL), mRNA. [Source:RefSeq mRNA;Acc:NM_174759]
Coordinates
chr11:93984123-93985858:-
Coord C1 exon
chr11:93985677-93985858
Coord A exon
chr11:93985539-93985676
Coord C2 exon
chr11:93984123-93985538
Length
138 bp
Sequences
Splice sites
5' ss Seq
AAGGTAATC
5' ss Score
7.46
3' ss Seq
CACTGCTGGTCCCCCCGCAGATG
3' ss Score
10.23
Exon sequences
Seq C1 exon
GTCCAAAAGGCGTGATCAATGACTGGCGCCGCTTTAAACAGCTGGAGACAGAGCAGCGGGAGGAGCAGTGCCGGGAGATGGAGAGGCTGATCAAGAAGCTGTCCCTGAGCTGCAGGTCCCATCTGGACGAGGAGGAGGAGCAGCGGAAGCAGAAGGACCTCCAGGAGAAGATCAGCGGGAAG
Seq A exon
GTAATCAGGAGCACCCAGGCCTCGCTCGGAAGCTGCCCCCGATCGCCAGCATTATTAGCATGGCGCCTCACACGTCTTGTGTAACCTGTGTCGCTGTCGGGTTTACATCTCTTACGCTCACTGCTGGTCCCCCCGCAG
Seq C2 exon
ATGACTCTGAAGGACTTGGCGGTGATGAACGAGGACCAGGATGATGAGGAGTTCCTGCAGCAGTACCGGAAGCAGAGGATGGAAGAGATGCGGCAGCAGCTCTACCAGGGGCCCCAGTTTAAGCAGGTTTTTGAGATCCCCAGTGGAGAAGGATTCCTGGACATGATTGACAAGGAGCAGAGGAGCACCCTCATCATGGTCCACATTTATGAGGACGGCATCCCAGGGACCGAAGCCATGAACGGTTGCATGCTCTGCCTGGCAGCAGAGTACCCGGCCGTCAAGTTCTGCCGGGTGAGGAGCTCAGTGATCGGGGCCAGCAGCCGCTTCACCAGGAATGCCCTCCCTGCCCTGCTCATCTACAAGGGGGGCGAACTGATTGGCAACTTTGTCCGAGTCACTGACCAGCTGGGGGAAGATTTCTTTGCTGTGGACCTTGAGGCTTTCCTCCAGGAGTTTGGATTGCTCCCGGAAAAGGAAGTGTTGTTGCGAACCTCTGTGCGTAACTCTGCCACCTGCCACAGTGAGGACAGTGATTTGGAAATTGATTGACCATCTGGGCCGGTGGCATAGACCCCTCATGGTTTGGGCTGGAAGACACATGTCCGCGTGTTTATTTTCATTCTTTTGTGTGATCTTCCGGCTTTTCCCCCTGTTCTTCATAGTTTCTTTTATGATATGTCAGGTCAAGAAATTCTCTGATCAAATCAGCGTGCTGAATCACCTTGTGGTTAGCCATGAAGTGACTTAACGTTGTATAAACAGGAAGCCAGGCTTTTGAACTGTTTACTTAAGATCCTCTAGCGTGACATCTCTGTTATTGTTTCTAGTCAATATTTACATAGCATCCTAAAGACAGTGTCCTGGAAATTGTCTTCAGATGGTCTCAGAGGTCTCTGCCAGGTCCGGGAGTATAATCCTATAGTTAGTGTGTTATTTGCAACATAAATACTACATTTCCTTCATCAATGATCATATTATATTCACGTGTAATCAGACTCATCGCCATAGAAGGCAGTTAAATTTTTTAACCCCGAGACCCTGTTCTCCCTAGGGTCTTGTTTAAAGGTTCTGGACCACATATGTTTGCCCCATCAACAGGGGTGACCTTTGCTGCTGGAGTCGATGTCCTGCTCAAGTGTTGTTAAGTCTACAGTAGGAGGAAGGATGGAGACGAACTTCCCTTTTGATGCTGGAAGACCAGCTTGATTTAAAAATTAGAGCTCGGATGGAGCTGGGAAGCCTTTTTAAAGAAAGATCTTTGAGTAAGATACCCCTGCTCACCTTTTCTCTTTTTCTCTTTTATTTAACAAGGTAAAATTTTTTTTGTTGTTTAATGTAGCTTTTGTTAATTTATTTTAATATTGGAAAAGTAACCAATATTCAAGAAAGGAAAATTTACCAAAATACAGAAGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000030675:ENSBTAT00000043370:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.475 A=NA C2=0.060
Domain overlap (PFAM):
C1:
PF0211411=Phosducin=FE(22.6=100)
A:
NA
C2:
PF0211411=Phosducin=PD(67.9=97.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCTGATCAAGAAGCTGTCCC
R:
AGGAATCCTTCTCCACTGGGG
Band lengths:
256-394
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development