RnoINT0038842 @ rn6
Intron Retention
Gene
ENSRNOG00000023148 | Col11a1
Description
collagen type XI alpha 1 chain [Source:RGD Symbol;Acc:2372]
Coordinates
chr2:217023415-217023855:+
Coord C1 exon
chr2:217023415-217023522
Coord A exon
chr2:217023523-217023801
Coord C2 exon
chr2:217023802-217023855
Length
279 bp
Sequences
Splice sites
5' ss Seq
CCGGTAAGT
5' ss Score
10.91
3' ss Seq
CTTTTGTAAAATCTCTCTAGGGA
3' ss Score
7.56
Exon sequences
Seq C1 exon
GGTCCCAAAGGAGAGAGAGGAGAGAAAGGAGAAGCTGGGCCCCCTGGTGCTGCGGGTCCTCCTGGTATTAAGGGGCCACCAGGTGATGATGGACCCAAGGGGAATCCG
Seq A exon
GTAAGTGTGTCCCCTTTAAAGTGATACTTGTACCCTTTTCATTTCTTAGCTTTTCATAGATAGACTAGAAATGTGGAGTTCTAGTGAAACAAATATCCTTATATCATTTTATATTTTCTCATTCATTCCTAGTTTATTTCAATTTTATCCATCTATTCTTCTATCTGGAGCACACATCTAATCAGTCTCTGATATAATTGTAATCTGTTGAAATAAAAATACACCATGGTGAAACTTCTCTTTTAATCTGTTTATTTTCCTTTTGTAAAATCTCTCTAG
Seq C2 exon
GGACCTGTTGGGTTTCCTGGAGATCCTGGTCCACCTGGAGAACCTGGTCCTGCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000023148:ENSRNOT00000068413:51
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:
NO
A:
NA
C2:
NO
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:
GGTCCCAAAGGAGAGAGAGGA
R:
TGCAGGACCAGGTTCTCCAG
Band lengths:
162-441
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]