RnoINT0039657 @ rn6
Intron Retention
Gene
ENSRNOG00000003357 | Col3a1
Description
collagen type III alpha 1 chain [Source:RGD Symbol;Acc:71029]
Coordinates
chr9:52040390-52041131:+
Coord C1 exon
chr9:52040390-52040434
Coord A exon
chr9:52040435-52041077
Coord C2 exon
chr9:52041078-52041131
Length
643 bp
Sequences
Splice sites
5' ss Seq
CCAGTGAGT
5' ss Score
8.28
3' ss Seq
AAATTGTACATTGGTTTTAGGGT
3' ss Score
5.93
Exon sequences
Seq C1 exon
GGTGCTCGAGGCAATGATGGTGCTCGGGGCAGTGACGGGCAACCA
Seq A exon
GTGAGTAACTTTGCATCCAATCCCGCTTTGTTCCTTATTGCTTCCAGATTGTGAATTACACATTACATTGCATTATATCATCCCATATTATACCGTTAGACAGCAAACCCATATTGCTTCTTCAGGATTATTTTTAACCTAGAAAATAAAAAACAATTTCTAGGTATAATACTAGATACTATCTGTCAAAATACAATTCAAACTGATATTGACCCTGTAAACTACGCCTCCTTGCAGTTCTGACCATTATTTTCAGTCATTCATTGACATGTATATGCCACTTGCGTTTTATATCCAATATTGGACATGCCACTTAAAAGAAATACAAAATAGATGGTGATACTCTCTCTGTGAAGTGAAGAGTACAAAAGCTCAGAGATAGATATCCCGTAACTCACAGGATTTATGAAGAAAGTGGATAGGAATCCTGTTGTTCTAACTGCAGATTTAACCCCTTATTATCTTACACAATGTTTCTCTGTAGAATCCTCCTGTGGGGATGGCAAACTCCATTTTATTTACATAGTTTCTTCTGTATTTTAGATTATTCATATATTATTTCATGGGAGGCTTCATGTGATGATTATTCTAGATGTTTAGTCTAACCAACTTTCCTTACATGCAAATTGTACATTGGTTTTAG
Seq C2 exon
GGTCCCCCTGGTCCTCCTGGAACTGCAGGATTCCCTGGATCTCCTGGTGCTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000003357:ENSRNOT00000004956:14
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(18.7=100)
A:
NA
C2:
PF0139113=Collagen=FE(22.7=100),PF0139113=Collagen=PU(7.2=27.8)
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]