RnoINT0040016 @ rn6
Intron Retention
Gene
ENSRNOG00000003736 | Col5a2
Description
collagen type V alpha 2 chain [Source:RGD Symbol;Acc:70921]
Coordinates
chr9:52134168-52134901:-
Coord C1 exon
chr9:52134848-52134901
Coord A exon
chr9:52134222-52134847
Coord C2 exon
chr9:52134168-52134221
Length
626 bp
Sequences
Splice sites
5' ss Seq
GATGTAAGT
5' ss Score
9.11
3' ss Seq
ACCTTCTCTTTCCCATTAAGGGT
3' ss Score
9.86
Exon sequences
Seq C1 exon
GGTCCAATTGGTGCCCGTGGACCAGAAGGCCCACCTGGGAAGCCTGGAGAAGAT
Seq A exon
GTAAGTTTCTATGGAACACTCCTTTGGAGTCTAAAAGAGGTTAACAAGGAGCTTCAAGGGCCAGGAGAGGATTCTGTTCTGATTCCTATTCATTTTCTCATTCCTTCAGCTCCTATTAAATCCACTCTAAAGTGGAGAACACAGGTTAAGGTTTTCCAAAATCAAGAAGGACTCTTTATTATGAGAGTGCTAAATTATTAAATTCTACATTGTATTCTCCAATAATTTTATTAATATTTATCTTTGAAAACAAATGAAAACCCAACTTTTTGTCCTTTAGAAGGCTAAAAAGAACTTACTCTGAACATCTAACACATGCTTATTTTACTTTTTACTGTGCTGGAATCAAATGGTGTATTGTGTATGATAGACAGGGTCTCTATTTTGAGCTGTGCCCAGCCCTTTGCACATAAATTCTGATGTTCTGAAAGTGGCAGATCCACTTTGCATCCATCTGTTCTCATTGATATCTTAAACAGTAGGATTAAGTGTTACCGGAGATAAAGCCTAGGTTCTGTTTTGCGACATAACACAAAACTTACTACAGACATTTCATCTGTAATTTGTCATGAAATCTCAGATTATAATAATCTCTCTATACATCTTACCTTCTCTTTCCCATTAAG
Seq C2 exon
GGTGAACCTGGAAGAAATGGGAATACAGGTGAAGTGGGGTTCTCAGGATCACCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000003736:ENSRNOT00000005073:11
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(26.6=100),PF0139113=Collagen=PU(19.0=83.3)
A:
NA
C2:
PF0139113=Collagen=PD(7.8=27.8),PF0139113=Collagen=FE(21.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
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]