BtaINT0109246 @ bosTau6
Intron Retention
Gene
ENSBTAG00000000445 | PDE6C
Description
phosphodiesterase 6C, cGMP-specific, cone, alpha prime [Source:HGNC Symbol;Acc:HGNC:8787]
Coordinates
chr26:14980383-14981734:+
Coord C1 exon
chr26:14980383-14980526
Coord A exon
chr26:14980527-14981665
Coord C2 exon
chr26:14981666-14981734
Length
1139 bp
Sequences
Splice sites
5' ss Seq
TTGGTAAGT
5' ss Score
10.47
3' ss Seq
CCTTTGCTTTTACATTTTAGAAA
3' ss Score
8.85
Exon sequences
Seq C1 exon
ACTCTCACACAGTTTCTTGGATGGTCTCTCTTAAATACTGACACCTATGAGAAAATGAATAAGCTGGAGAACAGAAAGGACATAGCCCAGGAAATGCTCATGAACCACACCAAGGCTACACCTGATGAGATCAAGTCTATTTTG
Seq A exon
GTAAGTGAGGAATTCAGTCCTACGGAGATTAGATGCTGTTTAACCATGGCTTCTGGATTTCACCGAAGTACCCAGAGGTGTGACAGCGGAAAATAAGTTTAGTCCTGGGCTGAGGAAGGGGAGACAGAGAAGGAGGGGTCAGGGAGAATTTGGGTGGTTCATAGTACACAGACCCTTACTGAATGTCCAGACTGCTTGGTTGGAACAGCTTTTTGTTTAAAATAGCTCTGTAGAAGCTGGAATAGTTAGGTCTAGATTGGACTGTTAGCACAGAAAAAAATATTTCCATGGAGGGAACCGTCAGCTGTTGGCCATGTAATACTCTATAACAATCGTAACCTCTCAGTTGTATATGACAATAAGCATCTATTTCTCATGCATTTATGGGTTGACCAGGCTTCGACTGATTTTGGTTGGGCTGTAAGCTGTGCATCTGGTTGGCTCTCTGCATCTGTCATCCTTGATCATCATACCTACCTGGTAGATGTTCTCATGATGATGACAAGTGGCAGACCGCAAGCCCAGCTGTGCAAGCTCATTTCAAGTCTTCCCTCATATCACATTCACTAAAATTTTCAGTGTACCAACATGACCAAATCAACATCATGGATGATTGGGGAGCCAGTAGGTATTTGCTAGAAGTGTTCTAATCACCACCAAATGAAGGGGAAATATCACACACCCATGATCTCTATTCCTTTATTTCCCTAGCTTTCAGAGAATGTGTGATATAGTTTTCCTGGGGTGTTTTGTTTGTTTTTGCTGGGTGGTTTGAGATGTAAAAGAAATTTGAGAATTTGATATGTTGAAGATGAAAATGTCTGGGGAAATACAGGGAAATTGCTATAAACTAATAGAAAAACAGATGTAAGCCACTCATTTTTCTCGCCTACGTGTGAACTATCAATGTCTCCTTCCTCTCTCTCTTTGAGACAGCTGCTGTTACATTTTGGAGGATAAGAAAGAGTAATTGTGTTTTAGAGAAAATTCTACATAATCCAGTGCTATAGACCTTTGTATGGCACTTTGTCATGGGACTCATTAGAGCATGCTTTATTTTAACTGATTTTAAGAGTAAAGGAATCACATAGAGATCAACTTTATAGGAATTTCACACTTCCTTTGCTTTTACATTTTAG
Seq C2 exon
AAATTTAAAGAGAAGTTAAATATAGATGTAATTGAAGACTGTGAAGAAAAACAGCTTGTCACAATTTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000000445:ENSBTAT00000000569:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.021 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0159021=GAF=PD(5.1=18.8)
A:
NA
C2:
NO
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:
CTCTCACACAGTTTCTTGGATGGT
R:
TGTGACAAGCTGTTTTTCTTCACA
Band lengths:
206-1345
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]