DreINT0007357 @ danRer10
Intron Retention
Gene
ENSDARG00000031678 | COL5A2 (2 of 2)
Description
collagen, type V, alpha 2 [Source:HGNC Symbol;Acc:HGNC:2210]
Coordinates
chr9:42861453-42861692:-
Coord C1 exon
chr9:42861639-42861692
Coord A exon
chr9:42861552-42861638
Coord C2 exon
chr9:42861453-42861551
Length
87 bp
Sequences
Splice sites
5' ss Seq
AAGGTAATA
5' ss Score
8.49
3' ss Seq
TATTTTGTTTCGGATCAAAGGGT
3' ss Score
3.4
Exon sequences
Seq C1 exon
GGGGCACCTGGAAACAGAGGCTTTCCAGGTCAAGATGGCTTACAGGGTCCAAAG
Seq A exon
GTAATAAGAGAGTTAAATTAGATACAAACTATTAACTTGCTGAATATGATTACCTGAATACTAAAATTATTTTGTTTCGGATCAAAG
Seq C2 exon
GGTGCACAAGGAGACCGTGGAACTTCAGGAACCTCTGGCCCTAAAGGTTCAACTGGTGATCCAGGAAGAACAGGTGAACCAGGTCTACCAGGAGCAAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000031678:ENSDART00000144744:24
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(19.8=100)
A:
NA
C2:
PF0139113=Collagen=PD(24.2=64.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGAAACAGAGGCTTTCCAGGT
R:
TCTTGCTCCTGGTAGACCTG
Band lengths:
144-231
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]