RnoINT0039609 @ rn6
Intron Retention
Gene
ENSRNOG00000058560 | Col2a1
Description
collagen type II alpha 1 chain [Source:RGD Symbol;Acc:2375]
Coordinates
chr7:139468152-139468540:-
Coord C1 exon
chr7:139468442-139468540
Coord A exon
chr7:139468197-139468441
Coord C2 exon
chr7:139468152-139468196
Length
245 bp
Sequences
Splice sites
5' ss Seq
TCTGTAAGT
5' ss Score
7.96
3' ss Seq
CTGTGCCATTTTCTTGTCAGGGT
3' ss Score
9.01
Exon sequences
Seq C1 exon
GGCGAAGCTGGTCCCACTGGTGCCCGTGGTCCTGAAGGTGCTCAAGGTTCTCGTGGCGAACCCGGCAATCCCGGATCCCCCGGGCCCGCAGGCGCTTCT
Seq A exon
GTAAGTTCACGTCTGTGGCCTGGAAGGCATGAATGACATCTGTGGCTTTGGCCCTCCTGAGTGCAATCTTTTGTAAAGTCCCAATCGCTGGGGTCCGATCACCTCCCACCCATTGTCCTCCCGCATGTCTCATGCCCCTGGAGCAGACAGCACTTGTCCCTGACCCCTAGACCGCGGCCTGATGGTAGGAATGGTTGGGTTGGTTCTTGGCTGTTGATTTTACCGCTGTGCCATTTTCTTGTCAG
Seq C2 exon
GGTAACCCAGGGACTGATGGTATTCCCGGAGCCAAAGGATCTGCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000058560:ENSRNOT00000086062:18
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(2.4=6.1),PF0139113=Collagen=FE(35.6=100),PF0139113=Collagen=PU(23.3=60.6)
A:
NA
C2:
PF0139113=Collagen=FE(15.6=100),PF0139113=Collagen=FE(16.3=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:
CGAAGCTGGTCCCACTGGT
R:
CAGATCCTTTGGCTCCGGGAA
Band lengths:
140-385
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]