RnoINT0038907 @ rn6
Intron Retention
Gene
ENSRNOG00000058470 | Col12a1
Description
collagen type XII alpha 1 chain [Source:RGD Symbol;Acc:2374]
Coordinates
chr8:87115658-87116008:-
Coord C1 exon
chr8:87115859-87116008
Coord A exon
chr8:87115778-87115858
Coord C2 exon
chr8:87115658-87115777
Length
81 bp
Sequences
Splice sites
5' ss Seq
TTGGTAGGT
5' ss Score
7.03
3' ss Seq
CATCTATGCGGTCATTTCAGCTC
3' ss Score
5.12
Exon sequences
Seq C1 exon
GGATGGAATGTCTCACCAGAGCTGAAGCAGACATTGTGTTGCTGGTGGATGGGTCATGGAGCATTGGCCGCGCAAATTTTAGAACTGTGCGAAGCTTCATCTCTCGTATCGTGGAAGTCTTTGAAATCGGCCCCAAGAGAGTACAAATTG
Seq A exon
GTAGGTCTCGTCAATGCTGAAGACCTTTGACAATTTACTTGCTACCTTTTATACATCGTAACATCTATGCGGTCATTTCAG
Seq C2 exon
CTCTCGCTCAGTACAGTGGAGACCCCAGAACAGAGTGGCACCTAAACGCTCATAGAGACAAGAAGAGTTTGTTACAGGCTGTGGCGAACTTGCCGTATAAGGGAGGAAACACCCTCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000058470:ENSRNOT00000077071:18
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.024
Domain overlap (PFAM):
C1:
PF0009223=VWA=PU(23.1=78.4)
A:
NA
C2:
PF0009223=VWA=FE(23.1=100)
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:
TCTCACCAGAGCTGAAGCAGA
R:
TCTGTTCTGGGGTCTCCACTG
Band lengths:
174-255
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]