BtaINT0109214 @ bosTau6
Intron Retention
Gene
ENSBTAG00000012945 | PDE6A
Description
phosphodiesterase 6A, cGMP-specific, rod, alpha [Source:HGNC Symbol;Acc:HGNC:8785]
Coordinates
chr7:63255133-63255995:-
Coord C1 exon
chr7:63255843-63255995
Coord A exon
chr7:63255223-63255842
Coord C2 exon
chr7:63255133-63255222
Length
620 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGA
5' ss Score
10.06
3' ss Seq
TCATGCTGTTTGATTTTCAGATT
3' ss Score
10.04
Exon sequences
Seq C1 exon
GATGAACATTTCTGTGACTTTGTGGACACCCTCACAGAGTACCAGACTAAGAACATCTTGGCTTCTCCCATAATGAATGGGAAGGATGTGGTGGCCATAATCATGGTTGTGAATAAAGTGGATGGGCCCCACTTCACCGAGAATGATGAAGAG
Seq A exon
GTAAGAGTGCTTAGGAACTGGTGGGCTGGCCATGCCAGCACATTCTCCCAGCTCACAAATCCTCTGACCCTTGCTATTTGCCCTGACCTTGGCTTTCCCCTCTGTAAGACAAGGAAGTTAGTGGTCTGATGATCTGTGAGGGAGGCAGGACAGGATAATCATTAAGATGTTGGGCTTTGGAGATAAGAATGTAGGGATAATGGTTCTGGTTCTGCTAATATCTGTTTGTCTTGGGCACGTTTTTCTGAACCTCAGATTACTTATTTGTAAAATGGGGCTGGTTTTATAGTATCTTTTATAGAGAGTATCTATAGTGTCTCTTGAGGTCATTTGTGGCCATCAGGATAACGTATATACATGACTTATCATGGGGCCTGCAAACTCAATGAACAGTAGCAACTTCTCATGAACACACTTCTAATAACATTAACATTCTACATTCTGTGAGTTTTACCCTCACATAATGCAACATTTTATGAGTCAGCTTTCCATGATCCATCTGCTCAAACTGTCTCAGATGAAGCTTTGAAAATATTCAAACTTATCAGCTGATGGTAGAAGTGGCCAGAAGAGGAATTTCTCCTTCTCATCTGTTTCTCCTCATGCTGTTTGATTTTCAG
Seq C2 exon
ATTCTTCTCAAGTACCTCAATTTTGCAAATCTAATCATGAAGGTGTTCCACCTGAGTTACCTGCACAACTGTGAGACTCGGCGTGGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000012945:ENSBTAT00000036662:2
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:
PF0159021=GAF=FE(33.3=100)
A:
NA
C2:
PF0159021=GAF=PD(8.0=40.0)
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:
GATGAACATTTCTGTGACTTTGTGGA
R:
CACGCCGAGTCTCACAGTTG
Band lengths:
238-858
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]