DreINT0007356 @ danRer10
Intron Retention
Gene
ENSDARG00000031678 | COL5A2 (2 of 2)
Description
collagen, type V, alpha 2 [Source:HGNC Symbol;Acc:HGNC:2210]
Coordinates
chr9:42861639-42861907:-
Coord C1 exon
chr9:42861800-42861907
Coord A exon
chr9:42861693-42861799
Coord C2 exon
chr9:42861639-42861692
Length
107 bp
Sequences
Splice sites
5' ss Seq
AGAGTGAGT
5' ss Score
7.36
3' ss Seq
TTTTTTATTCTCTAATAAAGGGG
3' ss Score
5.56
Exon sequences
Seq C1 exon
GGTCCACCAGGATCACAGGGAGTACTTGGACCTCAGGGAGAGGAGGGAAAACGTGGACCCAGAGGAGATCCTGGTTCTATTGGCCCACCTGGACCTGTTGGTGAGAGA
Seq A exon
GTGAGTCTAGTTTTACATTTTAATGCCTATGCAACAGCAAAATGACATGTATGAAATAGTGAAAATTACTTCAATTTTCAATGTTTTTTTTTTATTCTCTAATAAAG
Seq C2 exon
GGGGCACCTGGAAACAGAGGCTTTCCAGGTCAAGATGGCTTACAGGGTCCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000031678:ENSDART00000144744:23
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(26.0=54.1),PF0139113=Collagen=FE(39.6=100)
A:
NA
C2:
PF0139113=Collagen=FE(19.8=100)
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:
CCACCAGGATCACAGGGAGTA
R:
TGGACCCTGTAAGCCATCTTGA
Band lengths:
156-263
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]