RnoALTA0009784-3/3 @ rn6
Alternative 3'ss
Gene
ENSRNOG00000007657 | Col27a1
Description
collagen type XXVII alpha 1 chain [Source:RGD Symbol;Acc:735115]
Coordinates
chr5:79156313-79156643:+
Coord C1 exon
chr5:79156313-79156366
Coord A exon
chr5:79156520-79156599
Coord C2 exon
chr5:79156600-79156643
Length
80 bp
Sequences
Splice sites
5' ss Seq
CCCGTGAGT
5' ss Score
8.4
3' ss Seq
CCTCACCCATCCCCCTCCAGGCG
3' ss Score
9.93
Exon sequences
Seq C1 exon
GGTCAAGAGGGTGTTCAAGGCCTCCGTGGAGAACCAGGCCAGCAGGGCCAGCCC
Seq A exon
GCGGAGACTGGCCACCCTCCCCAGGAGAGAGGCCTGGGGCTGCCTTGAGTCATCTCACCTTGGTTTGCAGGGGCATCCAG
Seq C2 exon
GACCCCGGGGACGCCCAGGACCCAAAGGATCAAAAGGCGAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000007657-61-60,61-59,61-58-3/3
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
ORF disruption when splice site is used (sequence inclusion)
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(27.4=100),PF0139113=Collagen=PU(10.5=44.4)
A:
NA
C2:
PF0139113=Collagen=PD(22.6=77.8),PF0139113=Collagen=FE(22.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTCAAGAGGGTGTTCAAGGC
R:
TTCGCCTTTTGATCCTTTGGGT
Band lengths:
95-175
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]