DreINT0049478 @ danRer10
Intron Retention
Gene
ENSDARG00000020007 | col1a2
Description
collagen, type I, alpha 2 [Source:ZFIN;Acc:ZDB-GENE-030131-8415]
Coordinates
chr19:41400279-41400482:+
Coord C1 exon
chr19:41400279-41400332
Coord A exon
chr19:41400333-41400428
Coord C2 exon
chr19:41400429-41400482
Length
96 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
TTTTTTAATGTTTTCCAAAGGGT
3' ss Score
8.24
Exon sequences
Seq C1 exon
GGCAACAATGGCAGACCTGGAAAGCCTGGAGACAGAGGAGTCCTTGGAGCTCAG
Seq A exon
GTAAGAGAGTCATAGATGTGTAAATCAGTGATGTATGCATCTACCTTAGTAATATTTCTAACAAGGATCTTCATCTTTTTTTAATGTTTTCCAAAG
Seq C2 exon
GGTGCCCGTGGTTTCCCAGGAACTCCTGGACTTCCTGGCATGAAGGGACACAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000020007:ENSDART00000144544:9
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(8.2=33.3)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCAACAATGGCAGACCTGGAA
R:
GTGTCCCTTCATGCCAGGAAG
Band lengths:
104-200
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]