DreALTD0005642-3/3 @ danRer10
Alternative 5'ss
Gene
ENSDARG00000011407 | col2a1b
Description
collagen, type II, alpha 1b [Source:ZFIN;Acc:ZDB-GENE-050302-9]
Coordinates
chr11:109016-110298:-
Coord C1 exon
chr11:110245-110298
Coord A exon
chr11:110110-110244
Coord C2 exon
chr11:109016-109117
Length
135 bp
Sequences
Splice sites
5' ss Seq
AGCGTTTAC
5' ss Score
-25.16
3' ss Seq
CTCCTTCACTGTTGGTTTAGGGA
3' ss Score
7.64
Exon sequences
Seq C1 exon
GGTCCGCCGGGAGAACAAGGCCCACGCGGAGACCGGGGAGAGAAGGGGGAGAAG
Seq A exon
GTGGGCACCATTTCCTGCTGCGCTCGCGGCCTGTGTACTGACTGAAGACATCATTTATAGATAAACACACACCTCCAGTGCGCTCCACACAAACACACACACACACACACACACACACACACACACACACACAGC
Seq C2 exon
GGAAGTCCGGGCCCTCGGGGACGAGATGGAGAGCCGGGAACCCCAGGAAACCCTGGACCTCCAGGACCTCCAGGACCCAACGGACCACCAGGCCTTGGCGGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000011407-1-2,2-2,3-2-3/3
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
ORF disruption when splice site is used (sequence inclusion)
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(27.4=100)
A:
NA
C2:
PF0139113=Collagen=FE(53.2=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Human
(hg19)
No conservation detected
Mouse
(mm10)
No conservation detected
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:
GTCCGCCGGGAGAACAAG
R:
AAGGCCTGGTGGTCCGTT
Band lengths:
149-284
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]