GgaINT0010860 @ galGal4
Intron Retention
Gene
ENSGALG00000005628 | COL9A3
Description
collagen alpha-3(IX) chain precursor [Source:RefSeq peptide;Acc:NP_990636]
Coordinates
chr20:8717471-8718297:+
Coord C1 exon
chr20:8717471-8717525
Coord A exon
chr20:8717526-8718114
Coord C2 exon
chr20:8718115-8718297
Length
589 bp
Sequences
Splice sites
5' ss Seq
ACGGTGAGT
5' ss Score
11.45
3' ss Seq
ATTCTGTTTTTGCTTTTCAGATC
3' ss Score
11.62
Exon sequences
Seq C1 exon
GGCAAAGAGGCCAGCGAGCAACATATAAGAGAACTCTGTGGGGAAATGATAAACG
Seq A exon
GTGAGTTTTGCTGGGAGAAAACAAACCAATTATTGTGTGTGGCTGAAGATGAGATCTTGAACATGAGATGTCTACTGAGATTTGTGCTTTTTTATCTTAAGTAAGAAAAATACATTGGCTGTTAATGGATGGAAATTCTTCAGGAAATTCTTGTTGTTTGGGATGCCTTTCATTTTCTTGAGTTTAGTGTTTTTAAATGATTCAATGGGGCAACATACAAAGCATGCTGGCAGAAGCTCTGATATGTCGTTCAGAAGCTCAGCTCCTATAGCTTTCCTCTCCCCGCCATGGCACATCCCAGTCCTCAAAGCAGGGCTCCAGCCAGGTGCCAGCTCCCCAGCATCTGCCTTTCTTTCCTTGCTGTTACTGCTTTGCCTTTAGAGGTTATGTTCAGCATGGCTTGTTTCAGAGGACTTGGTTTTTAATTATTTAAGTATCATTTTCCAGAATACTCGCCTTGTTTCAAAGTGGCTTAGGAAACAGAAAACAGCATAAGGCAGCAGCAGGTTTCTGACCAAATGGCAAAGAGTGAAAATGTCGGACATGCAGTTTTTAATGTAGGTGCTGATATTCTGTTTTTGCTTTTCAG
Seq C2 exon
ATCAAATTGCACAGTTAGCTGCTAATCTAAGAAAGCCCTTATCTCCTGGGATGACGGGGCGCCCTGGTCCTGCTGGTCCACCGGGTCCTCCAGGAGCGACGGGAAGCGTTGGACATCCTGGTGCTCGTGGTCCACCCGGATACAGAGGGCCAACAGGAGAGCTTGGTGATCCTGGCCCCAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005628:ENSGALT00000009029:29
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=PD(7.9=26.3)
A:
NA
C2:
PF0139113=Collagen=PU(75.8=75.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGGCCAGCGAGCAACATATA
R:
CTGGGGCCAGGATCACCAAG
Band lengths:
230-819
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]