DreALTD0000762-2/2 @ danRer10
Alternative 5'ss
Gene
ENSDARG00000101258 | COL27A1 (2 of 2)
Description
collagen, type XXVII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:22986]
Coordinates
chr16:51912062-51914602:+
Coord C1 exon
chr16:51912062-51912111
Coord A exon
chr16:51912112-51912115
Coord C2 exon
chr16:51914558-51914602
Length
4 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCAG
5' ss Score
4.95
3' ss Seq
TCTCTTCTCTTCTCTTCCAGGGT
3' ss Score
12.93
Exon sequences
Seq C1 exon
GGAGAACAGGGTCCTGTTGGAGAAGCTGGAGCCAAAGGCTATCCTGGCAG
Seq A exon
GCAG
Seq C2 exon
GGTTTACCTGGTCCAATAGGGCCTGTTGGGCCGAAAGGTGCTCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000101258-5-5,6-5-2/2
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(20.0=100)
A:
NA
C2:
PF0139113=Collagen=PD(3.5=20.0)
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGGGTCCTGTTGGAGAAGCTG
R:
GAGCACCTTTCGGCCCAAC
Band lengths:
86-90
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]