DreINT0049432 @ danRer10
Intron Retention
Gene
ENSDARG00000020007 | col1a2
Description
collagen, type I, alpha 2 [Source:ZFIN;Acc:ZDB-GENE-030131-8415]
Coordinates
chr19:41400429-41400648:+
Coord C1 exon
chr19:41400429-41400482
Coord A exon
chr19:41400483-41400594
Coord C2 exon
chr19:41400595-41400648
Length
112 bp
Sequences
Splice sites
5' ss Seq
AGAGTAAGT
5' ss Score
9.35
3' ss Seq
CTTAATATCTTCCTCCTCAGGGT
3' ss Score
9.19
Exon sequences
Seq C1 exon
GGTGCCCGTGGTTTCCCAGGAACTCCTGGACTTCCTGGCATGAAGGGACACAGA
Seq A exon
GTAAGTTAGTAGTGTTGAGGACTGATGAGAAGACATAAGAAGCTGAAATTTGAGTTTTATTCATTTACCAAAAGAAGTCAAGGTCTCATGATCTTAATATCTTCCTCCTCAG
Seq C2 exon
GGTTACAATGGTATTGATGGACGCAAAGGAGAGCCTGGCGCAGCTGGTGCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000020007:ENSDART00000144544:10
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:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGCCCGTGGTTTCCCAG
R:
CAGGCTCTCCTTTGCGTCCAT
Band lengths:
90-202
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]