DreINT0049451 @ danRer10
Intron Retention
Gene
ENSDARG00000020007 | col1a2
Description
collagen, type I, alpha 2 [Source:ZFIN;Acc:ZDB-GENE-030131-8415]
Coordinates
chr19:41408468-41408756:+
Coord C1 exon
chr19:41408468-41408566
Coord A exon
chr19:41408567-41408648
Coord C2 exon
chr19:41408649-41408756
Length
82 bp
Sequences
Splice sites
5' ss Seq
AAGGTATGC
5' ss Score
9.55
3' ss Seq
ACAAAATGTGTATTATTCAGGGA
3' ss Score
6.04
Exon sequences
Seq C1 exon
GGAGAGCGTGGTAACCCTGGACCTGCTGGTGCTGCTGGCGCTCAGGGACCCATTGGTGCTCGTGGACCTTCTGGTACTCCTGGCCCTGATGGAAACAAG
Seq A exon
GTATGCAAACAGATTCACTACAAAAATGCCATCTAGATACTTTGTTTTTATTAGTATATCTGACAAAATGTGTATTATTCAG
Seq C2 exon
GGAGAGCCTGGTGCAGTTGGACCTGCTGGTGCCCCTGGACCACAGGGAGCTGCTGGTATGCCTGGTGAGCGTGGTGCTGCTGGCACCCCTGGAGCTAAGGGAGAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000020007:ENSDART00000144544:29
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(33.0=100),PF0139113=Collagen=PU(14.9=42.4)
A:
NA
C2:
PF0139113=Collagen=PD(29.9=80.6),PF0139113=Collagen=FE(37.2=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:
GAGAGCGTGGTAACCCTGGA
R:
CTCACCAGGCATACCAGCAG
Band lengths:
167-249
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]