RnoINT0040045 @ rn6
Intron Retention
Gene
ENSRNOG00000003736 | Col5a2
Description
collagen type V alpha 2 chain [Source:RGD Symbol;Acc:70921]
Coordinates
chr9:52148540-52149173:-
Coord C1 exon
chr9:52149148-52149173
Coord A exon
chr9:52148573-52149147
Coord C2 exon
chr9:52148540-52148572
Length
575 bp
Sequences
Splice sites
5' ss Seq
ATTGCTATC
5' ss Score
-29.08
3' ss Seq
TTTCCTTGTTTGGTGTTTAGGTA
3' ss Score
9.49
Exon sequences
Seq C1 exon
AAGGCTTACCAGGGTATTATGAAATT
Seq A exon
GCTATCATTTCAAACCACGGATTTTTATGGCAGTTTTTAATCAGTCTGTTATGGGAAAAGACTACACAGTTAATTATTTGGTGTTAAACATATTTTCACTTTACCTTTAAATTCCATTTCCTTAGTTTTTCTTAAAAGTAAACATTTCCTATAGTTTCCCCTTTTCATGTTTGATATATCTTAGATTCCAAATATCTGACATTTATTAAGACACGTAATTCTATGTGGTTATTTCCTACACACCATTTGCATTTGTGTCTTCCTGTAAATTTTCACTTGAAGAAGCTTAGTACACAGAGATTATGTAATCAGTTCAAGGTCACACAGTTGTCATGTGGGTGACACTCTGAGTGCAGTGTGGATGTTTCAGTTTCCATTGCAATTACTACATTCCTTTGTTAGCACTCAACCTAGATGACCTTTTAACTCATAAGGCAGGGGGAGTACAACTGGTTAGGAACACCTACATTCTTAAAAAGATTCTGCTGTGCTTTTGTTTTTATTCATCGGACTACTGAATTTTCCATTCCTTGTGTAAAACTTGGTCTTTACAAATTTCCTTGTTTGGTGTTTAG
Seq C2 exon
GTAACGGGCATACGTGGTCGTCCAGGACCTGCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000003736:ENSRNOT00000005073:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.111 A=NA C2=0.909
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0139113=Collagen=PU(12.9=72.7)
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:
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]