DreINT0048900 @ danRer10
Intron Retention
Gene
ENSDARG00000026165 | col11a1a
Description
collagen, type XI, alpha 1a [Source:ZFIN;Acc:ZDB-GENE-070209-167]
Coordinates
chr24:28768471-28768691:-
Coord C1 exon
chr24:28768629-28768691
Coord A exon
chr24:28768513-28768628
Coord C2 exon
chr24:28768471-28768512
Length
116 bp
Sequences
Splice sites
5' ss Seq
CCAGTGAGT
5' ss Score
8.28
3' ss Seq
GATTTTGGTGTGATTCAAAGGGA
3' ss Score
4.31
Exon sequences
Seq C1 exon
CTGGGTGGAGGTGCTGCTCTTGGTCAGAAAGGTGAGAAAGGAGAGCCTGCAGTGATTGAACCA
Seq A exon
GTGAGTAAAAAGTGAATTTCTTATATGCATCAACATGGGGACGATATTAATCTGAGTTTATTACATAATTTGATCATGCAATCTGTCAGTAATTGTGATTTTGGTGTGATTCAAAG
Seq C2 exon
GGAATGCTGATCGAGGGACCTTCAGGACCACCTGGACCTGCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000026165:ENSDART00000003503:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0139113=Collagen=PU(18.5=71.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGGTGCTGCTCTTGGTCAGA
R:
AGCAGGTCCAGGTGGTCC
Band lengths:
98-214
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]