RnoINT0039663 @ rn6
Intron Retention
Gene
ENSRNOG00000003357 | Col3a1
Description
collagen type III alpha 1 chain [Source:RGD Symbol;Acc:71029]
Coordinates
chr9:52032508-52032967:+
Coord C1 exon
chr9:52032508-52032707
Coord A exon
chr9:52032708-52032916
Coord C2 exon
chr9:52032917-52032967
Length
209 bp
Sequences
Splice sites
5' ss Seq
CCTGTGAGT
5' ss Score
7.21
3' ss Seq
ATATTTTTTACATGTTATAGGCT
3' ss Score
6.33
Exon sequences
Seq C1 exon
ATGAATTGGGATGCAACTACCTTGGTCAGTCCTATGAGTCTAGAGATGTCTGGAAGCCAGAACCATGTCAAATATGTGTCTGCGACTCGGGATCTGTCCTCTGTGATGACATAATGTGTGATGATGAGCCACTAGACTGCCCCAACCCAGAGATCCCATTTGGAGAATGTTGTGCAATATGTCCACAGCCTTCTACACCT
Seq A exon
GTGAGTCTGTAACATATATTAACTCTTCAAGAATCATATTTAAACACATAAATAGCATCTATAGTTTAAAGGCTTGAAAGAAATTGCCATGACAAATGAATAATGCCACTTTTAACAAAAAGGCGGGGATTGTGTGTAATCAGAATTAAGAAATAAAGGTGTCAATTGTGCCATAGTTTACACATCTCCATATTTTTTACATGTTATAG
Seq C2 exon
GCTCCTGTCATTCCTGATGGTAATAGACCTCAAGGCCCCAAGGGAGATCCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000003357:ENSRNOT00000004956:2
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=1.000
Domain overlap (PFAM):
C1:
PF0009313=VWC=WD(100=85.1)
A:
NA
C2:
PF0139113=Collagen=PU(24.5=70.6)
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:
TTGGGATGCAACTACCTTGGT
R:
GATCTCCCTTGGGGCCTTGAG
Band lengths:
244-453
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]