RnoALTA0009788-2/3 @ rn6
Alternative 3'ss
Gene
ENSRNOG00000007657 | Col27a1
Description
collagen type XXVII alpha 1 chain [Source:RGD Symbol;Acc:735115]
Coordinates
chr5:79164975-79165950:+
Coord C1 exon
chr5:79164975-79165040
Coord A exon
chr5:79165779-79165781
Coord C2 exon
chr5:79165782-79165950
Length
3 bp
Sequences
Splice sites
5' ss Seq
GAGGTACTG
5' ss Score
7.67
3' ss Seq
ATGGCCCTTTCTCTCTGTAGCAG
3' ss Score
9.1
Exon sequences
Seq C1 exon
CAACAAGATGACCTTGAGGCAGCTTTCCAAACGTGGATGGATGCTCACGGAGCAGTCAGATTGGAG
Seq A exon
CAG
Seq C2 exon
GGGTACAGCTATCCGGACCAGCTGATGCTAGACCAGGGAGGGGAGATCTTCAAAACCTTACACTACCTCAGCAACCTCATCCAGAGCATTAAGACGCCCTTGGGCACCAAGGAGAACCCAGCCCGGGTCTGCCGGGACCTCATGGACTGCGAACAGAAGATGGCGGATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000007657-79-80,79-79,79-78-2/3
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.273 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0141013=COLFI=PU(38.6=46.6)
Main Skipping 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:
TTGAGGCAGCTTTCCAAACGT
R:
GAAGATCTCCCCTCCCTGGTC
Band lengths:
104-107
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]