RnoINT0038823 @ rn6
Intron Retention
Gene
ENSRNOG00000023148 | Col11a1
Description
collagen type XI alpha 1 chain [Source:RGD Symbol;Acc:2372]
Coordinates
chr2:216979098-216979310:+
Coord C1 exon
chr2:216979098-216979151
Coord A exon
chr2:216979152-216979265
Coord C2 exon
chr2:216979266-216979310
Length
114 bp
Sequences
Splice sites
5' ss Seq
AAGGTATCA
5' ss Score
7.22
3' ss Seq
TTCCTTTGCTTTGTTGCCAGGGT
3' ss Score
6.9
Exon sequences
Seq C1 exon
GGTCCTCGAGGTTCCAGAGGCGCCAGAGGTCCCACAGGAAAACCTGGGCCGAAG
Seq A exon
GTATCATCCGAACTTACTGTGATTTGTGTTGCAAATCCTTGTAGAGGAACGAAGTCTGAGTAGCAGGTTCACCTTAGATTCTCTTTTCACACTTTTCCTTTGCTTTGTTGCCAG
Seq C2 exon
GGTACATCAGGTGGTGATGGCCCTCCTGGCCCACCAGGCGAAAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000023148:ENSRNOT00000068413:34
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.811 A=NA C2=0.750
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:
GGTCCTCGAGGTTCCAGAGG
R:
CCAGGAGGGCCATCACCA
Band lengths:
83-197
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]