DreALTD0005629-2/2 @ danRer10
Alternative 5'ss
Gene
ENSDARG00000099930 | col27a1b
Description
collagen, type XXVII, alpha 1b [Source:ZFIN;Acc:ZDB-GENE-100119-2]
Coordinates
chr5:64555343-64558949:-
Coord C1 exon
chr5:64558913-64558949
Coord A exon
chr5:64558905-64558912
Coord C2 exon
chr5:64555343-64555396
Length
8 bp
Sequences
Splice sites
5' ss Seq
CCGGTAAAG
5' ss Score
6.84
3' ss Seq
TCTCACATTTGTGTGCTTAGGGC
3' ss Score
9.14
Exon sequences
Seq C1 exon
GGTTTACCTGGTGTTCCTGGGAAGAAGGGCAAGATGG
Seq A exon
GTAGGCCG
Seq C2 exon
GGCTTTCCAGGAGATTTTGGGGAGCGAGGACCACCAGGACCTGATGGAAACCCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000099930-13-13,14-13-2/2
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(18.2=100),PF0139113=Collagen=FE(16.3=100)
A:
NA
C2:
PF0139113=Collagen=PD(5.2=22.2),PF0139113=Collagen=FE(19.8=100)
Main Skipping Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGGTGTTCCTGGGAAGAAGG
R:
TGGGTTTCCATCAGGTCCTGG
Band lengths:
84-92
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]