RnoINT0039677 @ rn6
Intron Retention
Gene
ENSRNOG00000003357 | Col3a1
Description
collagen type III alpha 1 chain [Source:RGD Symbol;Acc:71029]
Coordinates
chr9:52048089-52048745:+
Coord C1 exon
chr9:52048089-52048142
Coord A exon
chr9:52048143-52048691
Coord C2 exon
chr9:52048692-52048745
Length
549 bp
Sequences
Splice sites
5' ss Seq
AGAGTGAGT
5' ss Score
7.36
3' ss Seq
AAAGAGGCTTCTTTATGCAGGGT
3' ss Score
2.89
Exon sequences
Seq C1 exon
GGTGAGCCAGGCGGTGCGGGTGCTGATGGAGTTCCAGGAAAGGATGGGCCGAGA
Seq A exon
GTGAGTATTCACATAAATGAGAAATGAACCCTGGTTATATACAATGTATTGTAGACCCTTCTTCAGCTTTCACTGCTTCATTAAATGAGACCATATGTTACCACATTCTGAATATTAAAACACTGATCACTTGGCTGCTTAAATTTTTAGCTTCTATCCTGATAGTCCTACAGTGACCTAAGTTGAAGAGCTATGATACAAGCAAGGAATGGCTATCATAATGTATCAATGAAACCCAAAGCAATTAATATAGCCAAGAAATACAGTTTTAAAAAGATGTTACCATAAGATATTTTATCACATCCTCTTTGTTTTCGCTAATTAAGGTTTTAAAAAAGAATGAATCAATAAAATCACTTAGTTTTTTACCTTCTTCTACTATACCGACAGAATAGTGAACATACTAGACTCTCATATTTATACATAGCACTCATTTGAGCCACAAAAGAACAAAATCTATCACCTTAAGTAATAAAATGCCTCTATGCCCTGATTAATACAAGAAATGATGTTTATTTTTTTCAAAACTAAAGAGGCTTCTTTATGCAG
Seq C2 exon
GGTCCTGCTGGTCCTATTGGTCCCCCTGGCCCAGCTGGTCAGCCTGGAGATAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000003357:ENSRNOT00000004956:32
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:
NO
A:
NA
C2:
NO
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]