RnoINT0039305 @ rn6
Intron Retention
Gene
ENSRNOG00000003897 | Col1a1
Description
collagen type I alpha 1 chain [Source:RGD Symbol;Acc:61817]
Coordinates
chr10:82749573-82749840:+
Coord C1 exon
chr10:82749573-82749626
Coord A exon
chr10:82749627-82749786
Coord C2 exon
chr10:82749787-82749840
Length
160 bp
Sequences
Splice sites
5' ss Seq
TCAGTAAGT
5' ss Score
9.14
3' ss Seq
GCTTCACCTGTCTCCTCTAGGGT
3' ss Score
9.62
Exon sequences
Seq C1 exon
GGTCCTCAAGGTTTCCAAGGCCCCCCTGGTGAACCTGGCGAGCCTGGCGCTTCA
Seq A exon
GTAAGTTAGTCCTCCATGCAGACACTCCTCCCTCTCCACAAATTCTCCAGTGGAAGGTCACCCATACTGAGTGAGGGGTGGCTTGTCACCACCTAGTTCCAGTCTTCCTCCTTGTTGTCTCTCATCTTGGAGTTCTAACTGCTTCACCTGTCTCCTCTAG
Seq C2 exon
GGTCCAATGGGTCCCCGAGGTCCCCCTGGCCCTCCTGGCAAGAACGGAGATGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000003897:ENSRNOT00000005311:8
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=FE(27.4=100)
A:
NA
C2:
PF0139113=Collagen=FE(27.4=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:
GTCCTCAAGGTTTCCAAGGCC
R:
TCATCTCCGTTCTTGCCAGGA
Band lengths:
106-266
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]