BtaINT0109545 @ bosTau6
Intron Retention
Gene
ENSBTAG00000014069 | PDK4
Description
Bos taurus pyruvate dehydrogenase kinase, isozyme 4 (PDK4), mRNA. [Source:RefSeq mRNA;Acc:NM_001101883]
Coordinates
chr4:12764507-12766337:-
Coord C1 exon
chr4:12766196-12766337
Coord A exon
chr4:12764579-12766195
Coord C2 exon
chr4:12764507-12764578
Length
1617 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGT
5' ss Score
10.65
3' ss Seq
ACACACCTATTGCTTTGTAGGTA
3' ss Score
8.25
Exon sequences
Seq C1 exon
GTTCAGAAAACGCATGTGAAAGAACCTCGTTTGCATTTTTGCGACAAGAGTTGCCTGTGAGGCTGGCCAATATCCTGAAGGAAATTTATATACTCCCTGACCGACTAGTAAATACCTCTTCAGTGCAATTAGTTAAGAGCTG
Seq A exon
GTAAGTGGTGAACCATTCTGAAACAGTCTCTAGTTTTAAAACAGTTATCTGAGTATGAATTCTTACAATGTATTAAAATCTTAATTTGAAAACAGGTGGTCTGAACCTTAACTACTTAGCAAGATGTAAAGAATTTTCTGTTAATCTAGGGTAAGTTATCCTAAGGGCAGTTATGAAGCTGATAAAGTAGATATTTTCACAATATAATTTTTACCTCTAGAAGAAAATATGAAAAATAATCAACAGTTACCATATTTGTGTTTTAAATCATAAAAGAGTTTGATATTGCAAAAAGAATCCTATCCTAGAAATAGATATGGAATGACTACTATTTAGAGAGGGCTTAAAATGTCTTGCTGGCATTTGGCTATTACTATTCAGAAACTAAGTGGAGAGTCTGGCTAGAATTAAAAATTTGGGAGTATTCTGAATAAAAAAAAAGACATCAAAGATGGGGGCTTCCCTCATAGCTCAGTTGGTAAAGAATCGGCTTTACCAACTTTACCGCTTTGGTAAAGAAGACCCCGGTTCAATTCCTGGGTAGGGTAGATCCACTGGAGAAGGGATAGGCTACCCACTCCAGTATTCTTGGGCTTCCCTGGTGGCTCAGCTGGTAAAGAATGTGCCTGCAATGCGGGAGACCTGGGTTCGATCCCTGGGTTGGGAAGATCCCCTGGAAAAGGGAAAGGCTACCCATTCCAGTATTCTGGCCTGGAGAATTCCATGGACTGTATAGTCCATGGGGTCGCAAAGAGTCAGATATGACTGAGCAACTTTCACTCACTCACTCACTAATCTTCATTGCTTAAAAACCAACTAATGAAGCAGCCTCTGGATTCAAATCCCAGCTCTGTCCCTTCTTAGTTGTAAAAATCCTTGGTTAGTATCTCTATTATCTCTAAGCCTCAACCCCCTCCCCCCGTCTATTTTGGAGGAGAATAAAGATGATGCCTCAAAGGGATATTTGGGTGCAATTAAATGAGGTAATCCATGTACAAAGCACCGAGAACAGTGCCTGGCCCACAGCCAGCACTCAGTTCAGTTATGATCTCTTTTTCAAAATAAACACTGAGTTAGGGAGAGTACATAACCCAAAGCAGCAGATTTTCGGAGAACAGAGCCAGGTTATTCACCGAGGCAGATATATACCAGACCTTCGCCCTAACCCACCTTCTGCACAGCTCTCTGTTTATTGATTTAAGGAATATATGTATTATACAGTCATTAAACAGCTGCAATCTGAAACACAGACTCAATCCCTAGTATGTACTGCTGCTTTCAAGACTTCTACTCTCCTATGAACGCAGTAGGAAAAAAGCATGAAGCCTTCCCGTAAAAGTTGTTTCTAAACGATTTTGCTATAAAAATAAAGACTCCTGACAAACAAAACAGAAAACTGACTAGTGATCTGGGATAGTTAAAATTTTAAGTTATTAAGTTGAGGGTTAAATCGTTTTCTTTTTTCTAAGACATAATGTTTTCCAAATGTCTTGGAAGAAAGTTTTCATTTTAAATATACTTTCTCTCTTCAAATCTCTTGAAAGAAGCAATCTATTTTCAGCCACCTGTAACTGACTATTCCATTTTAAAACTTAAAACACACCTATTGCTTTGTAG
Seq C2 exon
GTATATGCAGAGCCTGATGGAGTTGGTGGAATTCCATGAGAAAAGCCCAGAGGACCAAAAGGCATTATCAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000014069:ENSBTAT00000038879:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF104364=BCDHK_Adom3=FE(28.7=100),PF0160215=Adaptin_N=PU(25.6=45.8)
A:
NA
C2:
PF104364=BCDHK_Adom3=FE(14.6=100),PF0160215=Adaptin_N=FE(27.9=100)
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:
GTTCAGAAAACGCATGTGAAAGA
R:
TCTGATAATGCCTTTTGGTCCTCTG
Band lengths:
214-1831
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]