DreINT0049444 @ danRer10
Intron Retention
Gene
ENSDARG00000020007 | col1a2
Description
collagen, type I, alpha 2 [Source:ZFIN;Acc:ZDB-GENE-030131-8415]
Coordinates
chr19:41406685-41406960:+
Coord C1 exon
chr19:41406685-41406738
Coord A exon
chr19:41406739-41406861
Coord C2 exon
chr19:41406862-41406960
Length
123 bp
Sequences
Splice sites
5' ss Seq
TCTGTGAGT
5' ss Score
7
3' ss Seq
ATTCATATGCCATATTTTAGGGT
3' ss Score
6.57
Exon sequences
Seq C1 exon
GGTCTCCCTGGTAGCCCTGGCAGTTCTGGACCCCCTGGAAAGGAAGGACCTTCT
Seq A exon
GTGAGTTCATGTTCATTTTACACATCTAGTTTTTGAGTGACCCAAAGTAATGTGTGAAAACATGCAAGCAATATGCAGAATGCTTTGCGAGCACTTAATACCAATTCATATGCCATATTTTAG
Seq C2 exon
GGTGCCGCTGGTCAAGATGGTCGCACCGGACCCCCTGGCCCAACTGGACCCAGAGGCCAGCCTGGTAACATTGGATTCCCTGGTCCCAAAGGACCTTCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000020007:ENSDART00000144544:22
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(25.0=100),PF0139113=Collagen=FE(19.8=100)
A:
NA
C2:
PF0139113=Collagen=PD(7.8=15.2),PF0139113=Collagen=PU(49.2=97.0),PF0139113=Collagen=PU(6.6=18.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCTCCCTGGTAGCCCTGG
R:
TCCTTTGGGACCAGGGAATCC
Band lengths:
146-269
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]