BtaINT0109252 @ bosTau6
Intron Retention
Gene
ENSBTAG00000000445 | PDE6C
Description
phosphodiesterase 6C, cGMP-specific, cone, alpha prime [Source:HGNC Symbol;Acc:HGNC:8787]
Coordinates
chr26:15001542-15003442:+
Coord C1 exon
chr26:15001542-15001642
Coord A exon
chr26:15001643-15003334
Coord C2 exon
chr26:15003335-15003442
Length
1692 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGT
5' ss Score
10.08
3' ss Seq
CACAGTTGTCTCTTTTTTAGGAA
3' ss Score
9.78
Exon sequences
Seq C1 exon
AGTTTAAACATATTCCAGAACCTAAATAAACGCCAGTATGAAACAGTTATTCATTTGTTTGAAGTTGCGATAATAGCGACTGACCTGGCTTTATATTTCAA
Seq A exon
GTAAGTACGGAACTCCCTTATACTCTGTGTGGTTCCGCCTTCCACGGTCCATGGCCTCAAAGTTAAAAGACATTTGTTTAGAGACACATTTCTTCATTTTCTTTTTGGATTACCAATAAATACCCTTAAGATAACTGATGGTGGATTTACTGGACATCTGGAAACATATTTTAAAAGCTAAGCCCCTAATATTAATTAGTTTGTTATCTGAAGAAACTTCAATTGAAGAATATGCATCAAAGTAGATACACTGCCAGAACACTGATGCTATAAAAGCTTACACGGTGCCTTTTGACCTGGGGAATTCATCATAGTTCGCAGTCTGGTATTTAGAGTTGCAGGCTTAGACATTTGATCCTGCCAGAGTCTGAGAGCTGAAAAATCTTAGTGATACTGACGCACATTAACAAACTAAAAAAATTTCTGAGTTACATACAGCAGAGGCATTAGCCTATTTATAATGATGATGATGATTACCAAGGAGACCAGATACTCCAAGCTTCTGTACATTTTCTTGTTGGTGAACTATAAAGTAAAATGCATTAGGACAAGGTGAACTAGTTACAGGGTCTAAATAGTTAACAACTTGGGCAGTATTAAATTATGCCTCTCCAATCCTTCATTAAAAATTCAATTATTAAATAGTTCAAACATGAAAGCAGATACTTCGAAATAGATAAGTGATATCCAAATAGCTATAGTCCAGATTCAACAAATGCTAAGATTTTGTCTTAGACATCTTTTCAAGGAAAGTGGTACAACTGAGGCATCCCGTACTCCATCATGAATGCCACACCCCCACCCCACTTCTTCACAAATACCACTGTCTTGGTATTGCTATGCATTCATCCTTCCCACTCATGTTTTCTATGGCATTACTAAGTGTTTAAAATTTTTCCATAAATGGTATCATACTGTATATACCTTTCTGCAACTTGTTTTCACACAACATTTTGAAGATTTAGCTTGGTGGTAAATTGAGATCCAGGTCATTCTTTTTAGATGTATATTCAACTGTGTGATTTTATCATAATTAATCTAGCCATTCTTCTATTCATGGACATTTAGATTATTCCCAGTTTTTCATCACTGCCTACATTGTGTATCTTTGTGTATATGAGTTTCTGTAAAGTACATATCTAGAAGTGGGACTGCTGTAGGGTTTGCATATCTTCAATTTTATACCACATGGCAAAACTCCTGCACTCCTTAGTAGGTACGCCAATTTAAACTCCTACCAGCAGTGTTACAAGAGTTCCTATTATTCCATATCTGGACTCTTCTTGATCTGGGCATATTTAAATATGTTTGTTAATGTGAGACAGAATATTATTATTCACACTTATAATTTTGTACCTTTTCATATATTTTACGTTCTAATATTTGGTTAGTTTTATACTTTACAATGTCTCATCACAACCTGTGGCCTTTGTTATGATCTTTTTGTCACATGTAGCTCTTAGTTTTAATGTATTTAAATTTACTTTTTTTTTTCCTTTCTGACTTGAGATTTTTCTGTCTTAAACCCTTTCTGTATCAAGGTTACACAGCCATTCCCTCTTCTCCTGCCTGGGTCCACAATGTGGACAACTGATGCAAAGTGGGAACATGAAACCTGAAAGGACATATTAAAGACACTTTAAACCTCTGGTCCTATATGCTAAAATTGTCGCACAGTTGTCTCTTTTTTAG
Seq C2 exon
GAAGAGAACCATGTTTCAAAAAATTGTTGATGCCTGTGAAAAAATGGAAACTGAAGAAGAGGCCATCAAATATGTAACCATTGATCCAACCAAAAAAGAGATTATCAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000000445:ENSBTAT00000000569:17
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(13.3=100)
A:
NA
C2:
PF0023314=PDEase_I=FE(14.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACATATTCCAGAACCTAAATAAACGC
R:
TTTTTGGTTGGATCAATGGTTACA
Band lengths:
190-1882
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]