GgaINT0010846 @ galGal4
Intron Retention
Gene
ENSGALG00000005628 | COL9A3
Description
collagen alpha-3(IX) chain precursor [Source:RefSeq peptide;Acc:NP_990636]
Coordinates
chr20:8706869-8707575:+
Coord C1 exon
chr20:8706869-8706922
Coord A exon
chr20:8706923-8707521
Coord C2 exon
chr20:8707522-8707575
Length
599 bp
Sequences
Splice sites
5' ss Seq
GCTGTATGT
5' ss Score
5.1
3' ss Seq
CTTTTCCCCTTTTGTCTCAGGGA
3' ss Score
10.42
Exon sequences
Seq C1 exon
GGTGACATCGGTTTCAGAGGGCCGCCTGGAATCCCAGGACCTCCGGGGAGAGCT
Seq A exon
GTATGTGCTGCTTTGTGGCCTTCCTTCCACAGCCAAAGCCTAATGTTTATCCTTTCTGAGCAGAGCCCTCCACTGCCAACGAACAGGAAGGAGATATACCAACTCCAGCAGATTATTCCCACCCCCTTTTTCCCTCCAGTTAAAGCAGTGCCATTTCACCTGACCCAGATCTCACAGTGCCTTTCCCTCTGTTGTGCCTTATTCTGTAGACTTGCCTGTGGATAGACCCCTGTACCCTCCTTAGTGTGCCCAAATACAAGACCAGATCTGCATCTGCAGAATTACGGCCTCTCTGAGAGCATTTCCCATCAGTTTTTCTCCGGCACTGTTTCTGGTGAAAGAAAATGTTCCAGTAAATGAAGGGGACGGCTGTGTCTGCCCTGAGGGATTGCTTGCAAAGTCCTTGCTGCAATTCATCCGTGTGTCAGGAATTACAGAGTGTAACAGAAAGTACAGCCCAGCTCCTAGGGGAGTGTGTACACTCACGCCTCTGCTAATGCTGGCAAACAGCACAAGAAAACCTTCATCATTTACACTCTGGAAGCATTAGTCTTTGAGGGCGATGAAAATACTTAATGGCTTTTCCCCTTTTGTCTCAG
Seq C2 exon
GGAGACCAAGGAAACAAAGGACCTCAAGGATTCAGAGGGCCCAAAGGCGATACT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005628:ENSGALT00000009029:15
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(27.0=100),PF0139113=Collagen=PU(2.1=11.1)
A:
NA
C2:
PF0139113=Collagen=PD(22.2=77.8),PF0139113=Collagen=FE(17.9=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Cow
(bosTau6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]