DreINT0049456 @ danRer10
Intron Retention
Gene
ENSDARG00000020007 | col1a2
Description
collagen, type I, alpha 2 [Source:ZFIN;Acc:ZDB-GENE-030131-8415]
Coordinates
chr19:41410378-41410614:+
Coord C1 exon
chr19:41410378-41410431
Coord A exon
chr19:41410432-41410560
Coord C2 exon
chr19:41410561-41410614
Length
129 bp
Sequences
Splice sites
5' ss Seq
CCTGTGAGT
5' ss Score
7.21
3' ss Seq
AGTTTTGTCATTTGTTTTAGGGT
3' ss Score
9.79
Exon sequences
Seq C1 exon
GGTGAGACTGGCTCCTTTGGTCCTCCTGGACCTGCTGGTCCTCGTGGTGCCCCT
Seq A exon
GTGAGTTTTCTATTCGTTTCTTTATTACTTCCATGATAAAGTTTTTTATCATACAAATTGTCCTATGACGTGCATTTGATATTCACATAACAATTAAGCACTCGACAAAAGTTTTGTCATTTGTTTTAG
Seq C2 exon
GGTGAGCGTGGTGAGTCTGGCCCTGCTGGACCTTCCGGTTTTGCTGGACCCCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000020007:ENSDART00000144544:33
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(12.0=55.6),PF0139113=Collagen=FE(19.1=100)
A:
NA
C2:
PF0139113=Collagen=FE(26.6=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:
GTGAGACTGGCTCCTTTGGTC
R:
GGGGGTCCAGCAAAACCG
Band lengths:
106-235
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]