RnoALTA0009786-2/2 @ rn6
Alternative 3'ss
Gene
ENSRNOG00000007657 | Col27a1
Description
collagen type XXVII alpha 1 chain [Source:RGD Symbol;Acc:735115]
Coordinates
chr5:79161344-79161895:+
Coord C1 exon
chr5:79161344-79161406
Coord A exon
chr5:79161805-79161841
Coord C2 exon
chr5:79161842-79161895
Length
37 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGT
5' ss Score
11.01
3' ss Seq
TCTGTCACTCTATTCCCCAGGCC
3' ss Score
9.43
Exon sequences
Seq C1 exon
GGTCCCCCTGGAGACATTGGCTTCAAAGGCATCCAAGGCCCTCGGGGTCCTCCTGGCTTGATG
Seq A exon
GCCCAGACCGAGGACTCATAGCCTCTTTCTCCTTTAG
Seq C2 exon
GGAAAGGAAGGTATCATTGGGCCCCCCGGAATGCTGGGACCTTCTGGACTCCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000007657-71-70,71-69-2/2
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=PU(12.7=38.1)
A:
NA
C2:
PF0139113=Collagen=FE(27.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
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:
GGTCCCCCTGGAGACATTGG
R:
AGTCCAGAAGGTCCCAGCATT
Band lengths:
113-150
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]