GgaINT0010861 @ galGal3
Intron Retention
Gene
ENSGALG00000005628 | COL9A3
Description
NA
Coordinates
chr20:8356748-8357234:+
Coord C1 exon
chr20:8356748-8356930
Coord A exon
chr20:8356931-8357156
Coord C2 exon
chr20:8357157-8357234
Length
226 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGA
5' ss Score
7.66
3' ss Seq
TTGTTTATTTATGATTCAAGGTG
3' ss Score
5.66
Exon sequences
Seq C1 exon
ATCAAATTGCACAGTTAGCTGCTAATCTAAGAAAGCCCTTATCTCCTGGGATGACGGGGCGCCCTGGTCCTGCTGGTCCACCGGGTCCTCCAGGAGCGACGGGAAGCGTTGGACATCCTGGTGCTCGTGGTCCACCCGGATACAGAGGGCCAACAGGAGAGCTTGGTGATCCTGGCCCCAGAG
Seq A exon
GTGAGACTGAGCTAAGCACTTTCTGTCTTATGCCCACTGAAATAAATGACCAACTTGGTATTGTTTCAGCAGTAGAGGAGAATAGATCGGTCTCTGGACAGACAGAGTTCTAGAGGATCATTTTGCTTGCATCTTCTAGGATGCTGTGCAAGCAAAGATCTTAGCACTGCCCTGAGACTTTTTGATTTTACAGCTCATGGCTGAAATTGTTTATTTATGATTCAAG
Seq C2 exon
GTGACACAGGCGAAAAGGGAGATAAAGGACCGGCTGGACAAGGAATTGATGGGCCTGATGGTGATCAAGGACCTCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005628:ENSGALT00000009029:30
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=PU(75.8=75.8)
A:
NA
C2:
PF0139113=Collagen=PD(22.6=51.9),PF0139113=Collagen=PU(24.6=59.3)
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:
TCAAATTGCACAGTTAGCTGCT
R:
CTTGAGGTCCTTGATCACCATCA
Band lengths:
260-486
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]