RnoALTD0007341-2/2 @ rn6
Alternative 5'ss
Gene
ENSRNOG00000007657 | Col27a1
Description
collagen type XXVII alpha 1 chain [Source:RGD Symbol;Acc:735115]
Coordinates
chr5:79131653-79131998:+
Coord C1 exon
chr5:79131653-79131706
Coord A exon
chr5:79131707-79131713
Coord C2 exon
chr5:79131945-79131998
Length
7 bp
Sequences
Splice sites
5' ss Seq
GGAGTAAGT
5' ss Score
8.57
3' ss Seq
TTTTTCTTCCTCCTTGGCAGGGC
3' ss Score
10.02
Exon sequences
Seq C1 exon
GGAGACCGTGGAGTGATGGGACCCCCAGGGGCACCTGGACCCAAGGGGTCGATG
Seq A exon
GTAAGGA
Seq C2 exon
GGCCATCCTGGAACACCTGGTGGTGTTGGGGACCCTGGAGAGCCTGGACCCTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000007657-37-33,38-33-2/2
Average complexity
Alt5
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(19.8=100)
A:
NA
C2:
PF0139113=Collagen=FE(21.5=100),PF0139113=Collagen=PU(12.8=55.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGACCGTGGAGTGATGGGA
R:
CTCTCCAGGGTCCCCAACAC
Band lengths:
95-102
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]