DreINT0049476 @ danRer10
Intron Retention
Gene
ENSDARG00000020007 | col1a2
Description
collagen, type I, alpha 2 [Source:ZFIN;Acc:ZDB-GENE-030131-8415]
Coordinates
chr19:41399999-41400198:+
Coord C1 exon
chr19:41399999-41400052
Coord A exon
chr19:41400053-41400144
Coord C2 exon
chr19:41400145-41400198
Length
92 bp
Sequences
Splice sites
5' ss Seq
GCTGTGAGT
5' ss Score
7.39
3' ss Seq
TATCTGTCATCTCTTTACAGGGA
3' ss Score
10.56
Exon sequences
Seq C1 exon
GGAGCTCAAGGACTGCAAGGACATGCTGGTGAGCCTGGAGAGCCCGGACAGGCT
Seq A exon
GTGAGTGCTCTCTGGTCAACACTGTGTTCACACGGTTTGGAAATTATGTTTGAACTTTAACACTGATTTCTCTATCTGTCATCTCTTTACAG
Seq C2 exon
GGAGCTATTGGTGCTCGTGGCCCTCCTGGACCCCCTGGCAAAAATGGTGAAGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000020007:ENSDART00000144544:7
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(23.3=100)
A:
NA
C2:
PF0139113=Collagen=FE(23.3=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:
GAGCTCAAGGACTGCAAGGAC
R:
TTCACCATTTTTGCCAGGGGG
Band lengths:
104-196
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]