DreINT0049447 @ danRer10
Intron Retention
Gene
ENSDARG00000020007 | col1a2
Description
collagen, type I, alpha 2 [Source:ZFIN;Acc:ZDB-GENE-030131-8415]
Coordinates
chr19:41407213-41407411:+
Coord C1 exon
chr19:41407213-41407266
Coord A exon
chr19:41407267-41407357
Coord C2 exon
chr19:41407358-41407411
Length
91 bp
Sequences
Splice sites
5' ss Seq
GCTGTAAGT
5' ss Score
8.56
3' ss Seq
ACATTTTGCTCCACTTTTAGGGT
3' ss Score
10.21
Exon sequences
Seq C1 exon
GGCAGCCCTGGTCCTGATGGTAACAATGGTCCTGCTGGTCCTGTTGGACTTGCT
Seq A exon
GTAAGTAGGCCATCTTGGTTCTATCAATGTAGATTAGCACATTACTTATTCCTGGTTCTCAATGGTAACAAACATTTTGCTCCACTTTTAG
Seq C2 exon
GGTGCCCCTGGTGAGAAAGGAGAGCAGGGACCCTCTGGTGCTCCTGGTTTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000020007:ENSDART00000144544:25
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:
PF0139113=Collagen=PD(20.0=72.2),PF0139113=Collagen=FE(18.7=100)
A:
NA
C2:
PF0139113=Collagen=FE(18.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGCCCTGGTCCTGATGGTAA
R:
TGGAAACCAGGAGCACCAGAG
Band lengths:
105-196
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]