DreALTD0005636-1/2 @ danRer10
Alternative 5'ss
Gene
ENSDARG00000099930 | col27a1b
Description
collagen, type XXVII, alpha 1b [Source:ZFIN;Acc:ZDB-GENE-100119-2]
Coordinates
chr5:64563386-64567461:-
Coord C1 exon
chr5:64567412-64567461
Coord A exon
NA
Coord C2 exon
chr5:64563386-64563424
Length
0 bp
Sequences
Splice sites
5' ss Seq
CAGGCAGGT
5' ss Score
2.53
3' ss Seq
CATTTTCTGTGTTTTTGTAGGGC
3' ss Score
10.51
Exon sequences
Seq C1 exon
GGAGAAAGAGGACCGGATGGAAGTCCAGGTGCCAAAGGTTATCCTGGCAG
Seq A exon
NA
Seq C2 exon
GGCTTACCTGGGCCTATAGGAAATATGGGACCAAAAGGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000099930-8-9,9-9-1/2
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
ORF disruption when splice site is used (sequence exclusion)
No structure available
Features
Disorder rate (Iupred):
C1=0.722 A=NA C2=0.278
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(26.2=100),PF0139113=Collagen=FE(22.1=100)
A:
NA
C2:
PF0139113=Collagen=FE(22.2=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGAGAAAGAGGACCGGATGGA
R:
GCCTTTTGGTCCCATATTTCCT
Band lengths:
89-93
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]