RnoINT0040024 @ rn6
Intron Retention
Gene
ENSRNOG00000003736 | Col5a2
Description
collagen type V alpha 2 chain [Source:RGD Symbol;Acc:70921]
Coordinates
chr9:52123704-52124180:-
Coord C1 exon
chr9:52124082-52124180
Coord A exon
chr9:52123749-52124081
Coord C2 exon
chr9:52123704-52123748
Length
333 bp
Sequences
Splice sites
5' ss Seq
CCTGTGAGT
5' ss Score
7.21
3' ss Seq
ATGGTTCATGTACATTTTAGGGT
3' ss Score
7.61
Exon sequences
Seq C1 exon
GGAGAAGCAGGTCCTACTGGGGCCCGAGGCCCTGAAGGACCTCAGGGACAGAGAGGTGAAACTGGGCCACCTGGTCCTGCTGGCTCTCATGGCCTTCCT
Seq A exon
GTGAGTTCCTAACATATCTAAAAGATAGCCCAGAAAGATGCTTATTCATTACGGTATCAGAAAAATGTAGCTTAGTTAATATAATCAATTCTGAGTTATTAGCATTCAAGAAAAAATACTTTACATGTCAATACAGCCTACTTTTTCTATCTTATGGAAAGGTTCCTAACAAAAAGTACTGTTATAATTATATAATTATATATAAATTATATATATATATAATAAAAATGTTAAATTTTGCAATTTTTTCTGCCTATTCTTAGGTGATCTGAATACTACTAGGTGTATCAGATATAGTTTAATATTTCAAAATATGGTTCATGTACATTTTAG
Seq C2 exon
GGTGCGGTGGGGACTGATGGTACACCTGGCGCTAAAGGACCCACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000003736:ENSRNOT00000005073:19
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=PU(27.0=60.6)
A:
NA
C2:
PF0139113=Collagen=FE(18.9=100),PF0139113=Collagen=PU(14.1=73.3)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]