DreALTA0008300-2/2 @ danRer10
Alternative 3'ss
Gene
ENSDARG00000026165 | col11a1a
Description
collagen, type XI, alpha 1a [Source:ZFIN;Acc:ZDB-GENE-070209-167]
Coordinates
chr24:28807255-28814144:-
Coord C1 exon
chr24:28813784-28814144
Coord A exon
chr24:28807417-28807419
Coord C2 exon
chr24:28807255-28807416
Length
3 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGG
5' ss Score
11.08
3' ss Seq
GTCTTTTCTACTCTGTTCAGCAG
3' ss Score
6.02
Exon sequences
Seq C1 exon
GCCCTCTTGACGGTGAGGCGATCGAGCGCTGCGCGTCTCATTTTGATTAAAGCCCGGATCCCTTCAGTCTGAAGGCTGGGCGCAAGGAAAGAAGGATCGAAGGGGGCCCGGCGAGACAAAATACCCCTCACCTATGGCTGTTTAGAGCAGATCGGGCACTTTTGGGATTGTAGAAGGGACGTCCTTTTCAAATAAGCAGAGCGTGCCCCGGGTTTTGTGCACATTTGTGGGCGCCCGACCATGGAGAGGCCAAGGTGGTCCCCAATGTGGAAAACGAAAAGGTGGCTTTTGGATTCCACTGTTTTCAAATTGATCACAGTTTCCCTCGTCCTGGTTCTGCAGGCTCCACATGTCAGAGCAG
Seq A exon
CAG
Seq C2 exon
AACCCGTGGATGTCTTAAAAGTATTAGAATTTCCCACTGTCCCAGAAGGAGTAGAGAAAACGTCAGGATTCTGCACAAACCGAAGAGCATCACAGCCAGACGCGGCCTACAAAATCAGCAAGAATGCCCAGCTCAGTGCCCCGACCAAGCAGCTTTTCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000026165-0-1,0-0-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (No Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.090
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
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:
CTGCAGGCTCCACATGTCAG
R:
TCGGTTTGTGCAGAATCCTGA
Band lengths:
108-111
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]