DreINT0049446 @ danRer10
Intron Retention
Gene
ENSDARG00000020007 | col1a2
Description
collagen, type I, alpha 2 [Source:ZFIN;Acc:ZDB-GENE-030131-8415]
Coordinates
chr19:41407036-41407266:+
Coord C1 exon
chr19:41407036-41407089
Coord A exon
chr19:41407090-41407212
Coord C2 exon
chr19:41407213-41407266
Length
123 bp
Sequences
Splice sites
5' ss Seq
AGAGTAAGT
5' ss Score
9.35
3' ss Seq
TAGTTTCTCTTGTTTCTTAGGGC
3' ss Score
8.33
Exon sequences
Seq C1 exon
GGCGAGGCTGGCAAGCCTGGTGAGAAGGGACCTGTTGGCCCTACTGGACTGAGA
Seq A exon
GTAAGTACTTCAGAGAGAGAGAGAGAGGGGGGATATCTGCTATAAACCTTGATCAGTATTCAGTATTAAGGAGTAAGTTATAAGCTATTGGCCACCTCTGATTTAGTTTCTCTTGTTTCTTAG
Seq C2 exon
GGCAGCCCTGGTCCTGATGGTAACAATGGTCCTGCTGGTCCTGTTGGACTTGCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000020007:ENSDART00000144544:24
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=FE(26.2=100),PF0139113=Collagen=FE(18.7=100)
A:
NA
C2:
PF0139113=Collagen=PD(20.0=72.2),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:
CTGGCAAGCCTGGTGAGAAG
R:
TCCAACAGGACCAGCAGGAC
Band lengths:
95-218
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]