GgaINT0050826 @ galGal4
Intron Retention
Gene
ENSGALG00000003923 | COL6A3
Description
collagen alpha-3(VI) chain precursor [Source:RefSeq peptide;Acc:NP_990865]
Coordinates
chr7:4790340-4790649:+
Coord C1 exon
chr7:4790340-4790402
Coord A exon
chr7:4790403-4790586
Coord C2 exon
chr7:4790587-4790649
Length
184 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGT
5' ss Score
9.25
3' ss Seq
GCCTCTCCTTTCTGTTCCAGGCT
3' ss Score
11.41
Exon sequences
Seq C1 exon
GGCCCACCTGGCCAGATTGGCACTCCAGGCATCAGGGGAGAGCAAGGCATCCCTGGGCCCAGG
Seq A exon
GTGAGTCCTTCTGCCCATTCCCAGCCAGGGAACCAACAGGGCTCAGCCTGGAGACCTCACTGGATTTCCTACAGTGCTTTGGCCCTAGTGGTTGATCCATGATTCCTATGGCCACGTAGATCCCTCATTTAAGGCACTCAGCTGTACTGACACAGTGCCAACGTGCCTCTCCTTTCTGTTCCAG
Seq C2 exon
GCTGGTGGTGGGCAACCAGGAGCACCTGGAGAAAGGGGCAGGATTGGCCCACTGGGACGAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003923:ENSGALT00000006250:26
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(31.7=100)
A:
NA
C2:
PF0139113=Collagen=PD(21.3=76.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Mouse
(mm9)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCACCTGGCCAGATTGG
R:
TTTCGTCCCAGTGGGCCAATC
Band lengths:
123-307
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]