RnoINT0038908 @ rn6
Intron Retention
Gene
ENSRNOG00000058470 | Col12a1
Description
collagen type XII alpha 1 chain [Source:RGD Symbol;Acc:2374]
Coordinates
chr8:87115394-87115777:-
Coord C1 exon
chr8:87115658-87115777
Coord A exon
chr8:87115559-87115657
Coord C2 exon
chr8:87115394-87115558
Length
99 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
TCTTTTAAAAATCCCACTAGGCA
3' ss Score
6.14
Exon sequences
Seq C1 exon
CTCTCGCTCAGTACAGTGGAGACCCCAGAACAGAGTGGCACCTAAACGCTCATAGAGACAAGAAGAGTTTGTTACAGGCTGTGGCGAACTTGCCGTATAAGGGAGGAAACACCCTCACAG
Seq A exon
GTGAGTCAGGATGCTTTGGTGAGGTTTTGGCATGTGCTTTTTGGTCAGGCAGGTAGCTGAGAGATGATGTGACTGGCTGTCTTTTAAAAATCCCACTAG
Seq C2 exon
GCATGGCTTTGAATTTCATTCGCCAACAGAGCTTCAAGACTCAAGCTGGCATGCGGCCTCGTGCTCGCAAAATTGGAGTTCTCATTACCGATGGAAAATCACAGGATGATGTGGAGGCTCCATCCAAGAAGCTCAAGGATGAAGGTGTAGAGCTGTTTGCTATCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000058470:ENSRNOT00000077071:19
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.024 A=NA C2=0.089
Domain overlap (PFAM):
C1:
PF0009223=VWA=FE(23.1=100)
A:
NA
C2:
PF0009223=VWA=FE(31.8=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:
TGGAGACCCCAGAACAGAGTG
R:
ACTCCAATTTTGCGAGCACGA
Band lengths:
183-282
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]