RnoINT0039303 @ rn6
Intron Retention
Gene
ENSRNOG00000003897 | Col1a1
Description
collagen type I alpha 1 chain [Source:RGD Symbol;Acc:61817]
Coordinates
chr10:82749080-82749416:+
Coord C1 exon
chr10:82749080-82749148
Coord A exon
chr10:82749149-82749371
Coord C2 exon
chr10:82749372-82749416
Length
223 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGC
5' ss Score
8.27
3' ss Seq
CCCTCTTTTTCCTTCTGTAGGGT
3' ss Score
12.35
Exon sequences
Seq C1 exon
AACTTTGCTTCCCAGATGTCCTATGGCTATGATGAGAAATCAGCTGGAGTTTCCGTGCCTGGCCCCATG
Seq A exon
GTGAGCCACCAGGGGGAGCAGTGGGACAAAGAGGAGGGGGATCCAAGAAAGGCCAACGATGTCCTGGGGAATAACTGGGGAAATAAAGGCCACCTTTGGGACTTCGGATCTAGAGAAGATGCAAGGCAGACAGCTGTGATCCCCACAGGAAGCAGTAGAAACAGATCTCTGATGCACTGCTTTTACTCACAGATATCACAAGCCCCTCTTTTTCCTTCTGTAG
Seq C2 exon
GGTCCTTCTGGTCCTCGTGGTCTCCCTGGCCCCCCTGGTGCACCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000003897:ENSRNOT00000005311:6
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(10.5=26.1),PF0139113=Collagen=PU(6.5=17.4)
A:
NA
C2:
PF0139113=Collagen=FE(22.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
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]