GgaINT0028817 @ galGal4
Intron Retention
Gene
ENSGALG00000006725 | ACAN
Description
aggrecan core protein precursor [Source:RefSeq peptide;Acc:NP_990286]
Coordinates
chr10:12564457-12565461:-
Coord C1 exon
chr10:12565392-12565461
Coord A exon
chr10:12564829-12565391
Coord C2 exon
chr10:12564457-12564828
Length
563 bp
Sequences
Splice sites
5' ss Seq
CAGGTACGT
5' ss Score
10.65
3' ss Seq
CTTTGTTTGGGAACTGGCAGACA
3' ss Score
2.58
Exon sequences
Seq C1 exon
ATGACCACTCTACTACTAGTGTTTGTGTGTTTGCAAGCCATCACCACAGCTGCCTCCGCAGAGCTCTCAG
Seq A exon
GTACGTGCTGCAGGGTGTGAGGAGTCAGCACTGAGCAAGGTGCTCCACACTGGTCCCATCACCAAATGGGGGCATCTCTAGGTGTGCCCAAGACTTGCTCTATGTATGCACGAGGCCCTTCTTTGGGTGGGTGTGATGCCACCATCTGTCACCTGTTCCATCATCATCTGTTACTGTGTTTGAGAGGATGGGGAGACAGTTCAGCCAAACAAGGGTTTATGGGGAAGTCAAGGGAATTTCAGCATTCCCCCTTTCTTCTGCCCTATCAGCTGTGATCTCACGTTGTGGACAGCAGCCACACTGCACGTAGGCCCCTTCACTCCATTCATCCCCACATTTGGCACTGCTCCCAACTCCCACACGCAACCATGGAGCAAGGGTAATTGTTGTAACCTCTATTTCTGCAAGGCTTTTTCAGCAGATTATGCAAAAAGGCCACACTTGAGAATGTAGGTGTAGGAGGCTTTCAAAGCAGATAGAGGCACTGTAGCACATGGAAGCGCTGGATATTTAGGATGAAGTGCATTGCTGATGTAACCCTCGCTTTGTTTGGGAACTGGCAG
Seq C2 exon
ACAGTAGCGATGGCCTGGAAGTGAAGATACCTGAGCAGTCTCCCCTGCGTGTTGTCCTGGGAAGCTCCCTGAACATCCCCTGCTATTTCAACATCCCAGAGGAAGAGGACACCAATGCTCTGCTGACCCCCCGGATCAAATGGAGCAAGCTTTCCAATGGAACAGAGATTGTCTTACTAGTGGCCACCGGTGGGAAGATCCGGCTCAATGCAGAGTACAGAGAGGTGATCTCCTTGCCCAATTACCCTGCCATCCCCACTGATGCCACCTTGGAAATCAAGGCGCTGAGATCCAACCACACTGGGATTTATCGCTGTGAAGTGATGTATGGGATTGAGGACAGACAAGACACCATAGAGGTCCTGGTGAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006725:ENSGALT00000010881:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0768612=V-set=WD(100=95.2),PF0019312=Xlink=PU(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGTTTGCAAGCCATCACCAC
R:
CCAGTGTGGTTGGATCTCAGC
Band lengths:
348-911
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]