GgaALTD1006545-1/2 @ galGal4
Alternative 5'ss
Gene
ENSGALG00000005797 | COL20A1
Description
collagen alpha-1(XX) chain precursor [Source:RefSeq peptide;Acc:NP_001004392]
Coordinates
chr20:9207437-9207883:+
Coord C1 exon
chr20:9207437-9207490
Coord A exon
NA
Coord C2 exon
chr20:9207830-9207883
Length
0 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAA
5' ss Score
8.38
3' ss Seq
GACTGGATTTGGTTTTGCAGGGG
3' ss Score
6.92
Exon sequences
Seq C1 exon
GGCATTCCTGGTGTGCAGGGAGCTCCAGGCAGAGATGGTCTTCAAGGTGCAAAG
Seq A exon
NA
Seq C2 exon
GGGGTGAGGGGACTGGAAGGCACAGCTGGGCCCCCAGGACCTCCTGGACCAAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005797-41-46,42-46-1/2
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(30.4=100)
A:
NA
C2:
PF0139113=Collagen=PD(23.2=72.2),PF0139113=Collagen=PU(28.3=94.4)
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg19)
No conservation detected
Mouse
(mm9)
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:
CATTCCTGGTGTGCAGGGAG
R:
CCTTGGTCCAGGAGGTCC
Band lengths:
106-297
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]