RnoINT0038806 @ rn6
Intron Retention
Gene
ENSRNOG00000023148 | Col11a1
Description
collagen type XI alpha 1 chain [Source:RGD Symbol;Acc:2372]
Coordinates
chr2:216949338-216949550:+
Coord C1 exon
chr2:216949338-216949391
Coord A exon
chr2:216949392-216949505
Coord C2 exon
chr2:216949506-216949550
Length
114 bp
Sequences
Splice sites
5' ss Seq
AGGGTATAC
5' ss Score
3.05
3' ss Seq
TCCATGTTTGTCACCCATAGGGA
3' ss Score
9.68
Exon sequences
Seq C1 exon
GGGGAAAGAGGTCCACAAGGTCCACCTGGCCTCCCCGGCGATGATGGAATGAGG
Seq A exon
GTATACTACGACTTTGCTTGTTTCAGACTTGTTTACAATTAGACCACCAAAGAACAAAGTTCTTTTGAAATCACACCCCTCTAACAGGACTCCGTCCATGTTTGTCACCCATAG
Seq C2 exon
GGAGAAGATGGAGAGATCGGGCCCAGGGGTCTTCCAGGGGAAGCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000023148:ENSRNOT00000068413:19
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(21.5=100),PF0139113=Collagen=PU(18.5=94.4)
A:
NA
C2:
PF0139113=Collagen=PD(13.8=60.0),PF0139113=Collagen=FE(18.4=100),PF0139113=Collagen=PU(20.6=93.3)
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:
AAGAGGTCCACAAGGTCCACC
R:
TTCCCCTGGAAGACCCCTG
Band lengths:
91-205
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]