RnoINT0039275 @ rn6
Intron Retention
Gene
ENSRNOG00000003897 | Col1a1
Description
collagen type I alpha 1 chain [Source:RGD Symbol;Acc:61817]
Coordinates
chr10:82754312-82754555:+
Coord C1 exon
chr10:82754312-82754365
Coord A exon
chr10:82754366-82754501
Coord C2 exon
chr10:82754502-82754555
Length
136 bp
Sequences
Splice sites
5' ss Seq
GTTGTAAGT
5' ss Score
8.3
3' ss Seq
TTATCACCTTCTCCCCACAGGGT
3' ss Score
12.45
Exon sequences
Seq C1 exon
GGAGAACCTGGAAAGGCTGGAGAACGAGGTGTCCCCGGACCCCCTGGCGCTGTT
Seq A exon
GTAAGTATCTCTTTTGAGTCTCTGTCACCATCCTCACATGGCAAGAGTCACTAGTGGGCTCTGCTGTGTCCCAGAGGTCCAGTCCCTACCTGCTGCTGCCATCTGCCACACTGAATTTATCACCTTCTCCCCACAG
Seq C2 exon
GGTCCCGCTGGCAAAGATGGCGAAGCTGGAGCTCAAGGAGCCCCCGGCCCTGCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000003897:ENSRNOT00000005311:26
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=PD(5.7=27.8)
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:
AGAACCTGGAAAGGCTGGAGA
R:
GCTCCAGCTTCGCCATCTTT
Band lengths:
84-220
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]