BtaINT0108835 @ bosTau6
Intron Retention
Gene
ENSBTAG00000004176 | PDC
Description
Bos taurus phosducin (PDC), mRNA. [Source:RefSeq mRNA;Acc:NM_001166527]
Coordinates
chr16:69009430-69012664:-
Coord C1 exon
chr16:69012513-69012664
Coord A exon
chr16:69010218-69012512
Coord C2 exon
chr16:69009430-69010217
Length
2295 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGA
5' ss Score
10.57
3' ss Seq
TTTCTTTCATCTATTCCCAGATG
3' ss Score
9.63
Exon sequences
Seq C1 exon
GACCCAAAGGAGTAATAAATGACTGGAGAAAGTTTAAATTGGAGAGTGAAGATAGTGATTCAGTTGCACCCAGCAAGAAGGAGATTCTCAGACAAATGTCTTCTCCTCAGAGTAGAGATGACAAAGACTCAAAAGAAAGATTCAGCAGAAAG
Seq A exon
GTAAGATAAGAAAAAAATCTATTATTTATTATTAACAATCTACAATATGTTTTTATTAAAGTATTGTTTGTATTAGCAAAAAAAAAAAAAGCAGGGGTGGGGGTGGGAAATGCAGTAAATGCCTTTGCCTATGAAGTCATCATAGGCAACTGTTAAAAGAATGAGTTACAAATACATGATCTGACTTAGAGGTAGTTCCACAATATGAGAAAGCAAGATGCAGAAAGTTATGTGATACCATTTTCTAGAGCAATAGAAAACAAACACTGTATTTGTATTTATGCTGAAATGATTATATGAGCATATATGTAAAAAAGTACAAAAAGACACTGACCAAACTGACAATATTGGTTAAGTGGAAGGGTGGGGTTCATTGACAGTTCTCAGCTTCCTCCTTCCAAGGAGGAGGAAGAAGGTAAGCAGAATAAGCCGCAATATATCCATGATTTTTTTTAAAGGAGCATTTTAAAAAATTCTCATTTGTCTCTTAGTATATAATGTGTATGTAAATCAGTATTTGTGGTTCAGTCTGTTTAACAGAGAACTATGATAGCAACTTCGGAGAAGGCAATGGCACCCCACTCCAGTACTCTTGCCTGGAAAATCCCATGGGCGGAGGAGCCTGGTAGGCTGCAGTCCATGGGGTCCCTAAGAGTCGGACACAACTGAGCAACTTCACTTTCACTTTTCACTTTCATGCATTGGAGAAGGAAATGGCAACCCACTCCATGTTCTTGACTGGAGAATCCCAGGGATGAGGGAGCCTGGTGGGCTGCCGTCTATGGGGTCGCACAGAGTTGGACACGACTGAAGCGACTTAGCAGCAGCATGATAGCAACTTACAAATTATACAAAACATTTAACAATGGTTAGGGTTAAAATAAATTAATTTGGAAAGACAAACTTAAAGCAGAAAAAATAATATGATAAGAAGAATGAGATAAAAAAAAGAGAATAAGGACATTAGAAAAACAAATATAGGAGGAAGAAACAAGAGAACAACGAAAGCACCAGATATTTCTACTTAATCCTGGTATCTTCTATAAAAAACCTACCTCATAAGTTTATTGTGAAGATCAAGAAAATAATCTATATAAATTATCTAATAAATAGCAAATTTTCCATGAATTTGGAGGTCACCCAACTTCCATGGTTCTGGGCTGCTCCACATCAATTAATCACACTATATCCCATCAACACACACTCCCATCGTGTGTGTGTGCATGTGTGTGTGTGAAGGGAGAGGGTGTTTAAAATTCTATTGCCTAAATCATAATGACATTGCAATTAAGAAAGCCTCTGCAGGTAATTTTATATTCCAGCTGCAGTGAAAAGTAGCTGTCTTGCAAATAGAAGTTAGGTCTTTTCTCATTTTAGCCTAAACCAGTGCATACAAATCACCAGGAGGGCTTGTTTAAACATGGCTCACTCAGCCTCACCCTGCCAGATTCTGATTCAGTAGATCTGGGGTGGCGCCCCCAAACTCGCGTTTCCCAGAACTTTTTGGCTGGTCGTGATGCCACCAGTCTTCTGGCTCATCTGGTGAACTCCAAATGTTGGTAAAAGCTGTCTTGCTTAAATGCCATCCTACAGATTCCAAAAAAACCAGTAAGTGATTAGACAAAATCTTTTAAACAACTTTTGTTGAGGAGGCAATAATGTCCAAAGGCATTTGTTGGGGACCCATTTAAATGAGTGTGCAGGCACTTGTGTGCACATGTGTGTATTTACAGTTTTATGAAAGTCACTCTAAAGTAGACCTTGCTGGGTTTTTTTTCACCCAAACTGGAATATTCCACGACCATCTCACAGCTCAACTATATTCAGCAATACTAATGTATGCATTTAATCATGAAATAATTACTGAACCTCTATTATGGGCCAGACACAAAACATATTAGAGAGTGATGAATGACACACAAAAAACTCCTGCCCCCACAGAACACAAAAGTTAGGAAAACTAATATGAGACAAATAAATATATATAATGATATCAAGTATTATTTATTACTATGAAGAAAAATAATAAAGCAAAAGGGGTACTAAGTGTGGGGCAGGGACACTTTTAGGTACAATAATCAAAGAAGGTGACATTTGAACAAATGAGGTGGAAGAAAAGGCCACCTCAGGAGGTAGTGAAAGTGAGTCACTCAGTCGCGTCCGACTCTTTGCGACCCCGTGGAGGTAGAGGAGACAGCAAATGCAAACTCTTAAAGTTGAGAACAGGTTTGTTATGTATAAGGAATACAAATTTCTGACTGATTGATCTCTATCATTTCTTTCATCTATTCCCAG
Seq C2 exon
ATGAGCGTTCAAGAATATGAACTAATCCACAAAGACAAAGAAGATGAAAATTGCCTTCGTAAATACCGCAGACAGTGTATGCAGGATATGCACCAGAAGCTGAGTTTTGGGCCTAGATATGGGTTTGTGTATGAGCTGGAATCTGGGGAGCAATTCCTGGAAACCATTGAAAAGGAACAGAAAATCACCACTATCGTTGTTCATATTTATGAAGATGGTATTAAGGGCTGTGATGCTCTAAACAGTAGCTTGATATGCCTTGCAGCCGAATACCCTATGGTCAAGTTTTGTAAAATAAAGGCTTCTAATACAGGTGCCGGAGACCGCTTTTCCTCAGATGTACTCCCCACGCTGCTTGTCTACAAAGGTGGGGAACTCCTAAGCAATTTCATTAGTGTTACTGAACAGCTGGCTGAAGAATTTTTTACTGGGGATGTGGAGTCTTTCCTAAATGAATATGGGTTATTACCTGAAAAGGAGATGCATGTCCTAGAGCAGAGCAACATGGAAGAGGATATGGAATAAAGATTCACTATGTCAATGTTTCATATTTCGTATTTCTCCTTTAAGCATTGAACACTGATTTTGGTAGTATTCACATTCTTTTAGGGAATACCAAACATAGCCCTGGCTTTTCTAATTTGGGGAAGAAAAACTCCAGACTGACACTAAAATTATATGATTAGCATGTCTTAATATTAGTTACTCAAGCTGATATAACACTTTACCTCAAAACATTGTAGTCTTCAGCAATATGTTAGTAGACAAAGAGAATATGAAAAATACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000004176:ENSBTAT00000005468:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.549 A=NA C2=0.057
Domain overlap (PFAM):
C1:
PF0211411=Phosducin=FE(20.4=100)
A:
NA
C2:
PF0211411=Phosducin=PD(70.6=98.9),PF141751=YaaC=WD(100=36.6)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development