BtaINT0109208 @ bosTau6
Intron Retention
Gene
ENSBTAG00000012945 | PDE6A
Description
phosphodiesterase 6A, cGMP-specific, rod, alpha [Source:HGNC Symbol;Acc:HGNC:8785]
Coordinates
chr7:63214478-63216155:-
Coord C1 exon
chr7:63216046-63216155
Coord A exon
chr7:63214566-63216045
Coord C2 exon
chr7:63214478-63214565
Length
1480 bp
Sequences
Splice sites
5' ss Seq
GAAGTGAGT
5' ss Score
7.97
3' ss Seq
TCTCTTTCTCTCCCATTCAGATC
3' ss Score
12.3
Exon sequences
Seq C1 exon
ACCGGAAAGCTGAAGCGATACTTCACAGACCTGGAGGCCTTGGCCATGGTCACCGCCGCCTTCTGCCACGACATTGACCACAGAGGCACTAACAATCTCTACCAGATGAA
Seq A exon
GTGAGTCAGCCCTTACTGGCCCTTCTCTCTACCTCCTGCCTCTGGGATTGATTACCTAGATCTGAATGGGTCTTAGACAGACTCACTTGCCATGGGGAATTCCCACGGTCCACAGCTTCCCACTTCCTCCTATCCTTTGGTTCTGGGTAAACTCCTGTGATAGAATAATGAAGCTCAAATATGTCTACACCCCAGTGCCTGGGGCCTGGGGATAAGTTGCCTTACATTCAAAAGAAACTTCATAAACATGATTAAGGATGTTGAAATATAGGGATTATCTTGGGTTATCCAAGTGGGCCCCAAATAGTTAGAAGGGTCCTTGTAAGAAGGAGGTAGGAACTCAGGGAGGACAGAAGATGCTACACTGTTGGCTTTGAAGATGCAGGATAAGTCACAAGCCAAGGAATTAGGGGCCTCTAGAAGCTAGAAAAGGCAAGGAAACAGTCTCCTCTAGAACCTCCAGAAGGAAAACAGCTCTTCAGACCATTTTAGACTTCTAAACTCCAGAGCTGAAAGACACTAAATTTTTCTTGTTTTAAGCCATTTAAGTTTGTGGTGATTTTCTAGAGCAGCAACAGGAAACTAATAAACTTTCTCATTCTGCTCCTTCCTCTCCTACTGAACTAATTTAAGCCAAGATGTTAGTAACTGCTAATGATTCATTTATTCACCTTAGGTTTATAATGCACAAAAGGCCAGCATGGTAGGCCCTATGTTAGGCAAAGGAGGTTCCATGGTGAACAAACCAGACACAGTCCCTGACTTCACAGAGCTTATATCCTAGTCTCTGAAGTAGTGGCCAGGAACCATGGTCTTGGGAGACCCTCATGACCACCACGTGGACTGGCAGAGCAGGGACTAGTGTCGTACCCAGGCTCTGCCCAGGGCCCACAGACTGTAAGTCATGCTTCTGTGAGTCTTCTCAGTTTCTGCCTGCTGCTCCAAGGTTAGAGATTATGTTTACATTTTACCTTGTAGAAGGCGAAGTACTGATCTCAGTGCTTGGCACACAACAAGGGCTCAGCAAATATTTATTGAATAAAGACGTGAATAAATACGTTGCTTGTGGGAATCCAGTGACTTCTCAGAATCAGGTTTGGAAGATCTGGGGCTCGGCGATCTTTAAAGCACTAGCCCAGTGCCAGTGTCCATGGATGGCTATGGGGATGGGTCTGTAAAACTGCACATGGCATTGTGTTTGTGTCTTTTTCTGGGGATAAGGGTCCACACTTCTAGGGAGGCCATGTCCCCAAAGAGGCCCAGAATTAGTTATGGAGAAAGTTAAAGTATGAGAGCCAGGACACCTGCTATCTAGTCCTATTTCTCACGGTCGTACTGTGTGACAAGTCCCTTCTTATTCTTGCACTTCAACCTATCTGCCTGCAGAATTAGGAGGTGACAGGAATGGATGATGCCTTTAACCTTCATCTCTGCCATTCCATGTTAATCTTCTCTGTGTGTCTCTTTCTCTCCCATTCAG
Seq C2 exon
ATCCCAGAACCCACTGGCCAAGCTCCATGGGTCCTCCATCTTGGAAAGACACCACTTGGAGTTTGGTAAAACACTCTTGAGAGATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000012945:ENSBTAT00000036662:14
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:
PF0023314=PDEase_I=FE(14.5=100)
A:
NA
C2:
PF0023314=PDEase_I=FE(11.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGCGATACTTCACAGACCTGGA
R:
TCATCTCTCAAGAGTGTTTTACCA
Band lengths:
184-1664
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]