RnoINT0038852 @ rn6
Intron Retention
Gene
ENSRNOG00000023148 | Col11a1
Description
collagen type XI alpha 1 chain [Source:RGD Symbol;Acc:2372]
Coordinates
chr2:217042405-217042593:+
Coord C1 exon
chr2:217042405-217042458
Coord A exon
chr2:217042459-217042557
Coord C2 exon
chr2:217042558-217042593
Length
99 bp
Sequences
Splice sites
5' ss Seq
CCAGTAAGT
5' ss Score
9.09
3' ss Seq
TGTTTCTTTGTGTTTTCTAGGGT
3' ss Score
11.97
Exon sequences
Seq C1 exon
GGCATCCCAGGTCCTGCTGGTCCCATAGGTCCTCCTGGTCCTCCAGGATTACCA
Seq A exon
GTAAGTACAAGACAATGGAAATATGAGGTAAACAGCAAGTATGCCAATGTAACCTATTGTCCTCGTGTTTACCTGTGTGTGTTTCTTTGTGTTTTCTAG
Seq C2 exon
GGTCCTGCTGGTCCGAAGGGTAACAAAGGATCTTCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000023148:ENSRNOT00000068413:60
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(20.8=88.9),PF0139113=Collagen=FE(27.0=100)
A:
NA
C2:
PF0139113=Collagen=FE(17.5=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:
ATCCCAGGTCCTGCTGGTC
R:
AGAAGATCCTTTGTTACCCTTCGG
Band lengths:
87-186
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]