DreALTD0005595-2/2 @ danRer10
Alternative 5'ss
Gene
ENSDARG00000019601 | col12a1b
Description
collagen, type XII, alpha 1b [Source:ZFIN;Acc:ZDB-GENE-120215-116]
Coordinates
chr20:49811581-49815163:-
Coord C1 exon
chr20:49814917-49815163
Coord A exon
chr20:49814897-49814916
Coord C2 exon
chr20:49811581-49811773
Length
20 bp
Sequences
Splice sites
5' ss Seq
CACGTACGT
5' ss Score
8.98
3' ss Seq
GCTTTCTGTTTGTCCTGCAGTGT
3' ss Score
10.19
Exon sequences
Seq C1 exon
CCTCTGCATCTGCCAAGGCTTTACTGGTGTCTGATGAAACCGAACGAACCATGCGGGTGATATGGAAAGCTGCTCCTGGTCCTGTGGTCAACTACAGACTAACGTACATCCCTCAGACCGGCGGTAAAGAGATGACAATGAAAATTCCTGCCAACGTCACCTACACCATGCTGAGGAAACTGCAGCACACCACCACCTACTTCATCACCGTGCATCCTATATACAAACGGGGAGAAGGAAAAGCAAG
Seq A exon
GCAAGGAGTAGGAACCACAC
Seq C2 exon
TGTCTCCATATAAAGCCCCAAGAAACCTACAGACCTCCGAACCCACCAAAACCAGTTTCCGAGTGACGTGGGACCCCGCTCCCGGTGATGTGCGGGGATACAAAGTCACCTTTCATCCCAGCGAAAATGATATTGATTTGGGAGAACTTCTTGTTGGACCATACGACAACACGGTTGTCCTTGAGGAACTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000019601-15-16,16-16-2/2
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.153 A=NA C2=0.392
Domain overlap (PFAM):
C1:
PF0004116=fn3=WD(100=88.9)
A:
NA
C2:
PF0004116=fn3=PU(74.1=92.3)
Main Skipping Isoform:
NA
Other Skipping Isoforms:
NA
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:
CCACCTACTTCATCACCGTGC
R:
TCGGAAACTGGTTTTGGTGGG
Band lengths:
117-137
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]