GgaALTD0006311-1/2 @ galGal3
Alternative 5'ss
Gene
ENSGALG00000016292 | COL21A1
Description
NA
Coordinates
chr3:90045240-90055522:+
Coord C1 exon
chr3:90045240-90045294
Coord A exon
NA
Coord C2 exon
chr3:90055469-90055522
Length
0 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGC
5' ss Score
9.26
3' ss Seq
TCTTGGTTCCTTTTTTTTAGGGT
3' ss Score
10.78
Exon sequences
Seq C1 exon
GGAGATCCTGGGCAGCCTGGGAATCATGGTTATCCTGGTCAGCCTGGTCCAGATG
Seq A exon
NA
Seq C2 exon
GGTTATCAAGGATCAGCAGGAACTCCAGGTATCCCAGGAACTCCAGGGGTTCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000016292-8-11,9-11-1/2
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
ORF disruption when splice site is used (sequence exclusion)
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(34.5=100),PF0139113=Collagen=PU(0.1=0.0)
A:
NA
C2:
PF0139113=Collagen=FE(29.3=100),PF0139113=Collagen=FE(20.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCAGCCTGGGAATCATGGTTA
R:
TTGAACCCCTGGAGTTCCTG
Band lengths:
98-106
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]