RnoINT0038847 @ rn6
Intron Retention
Gene
ENSRNOG00000023148 | Col11a1
Description
collagen type XI alpha 1 chain [Source:RGD Symbol;Acc:2372]
Coordinates
chr2:217029229-217029933:+
Coord C1 exon
chr2:217029229-217029336
Coord A exon
chr2:217029337-217029879
Coord C2 exon
chr2:217029880-217029933
Length
543 bp
Sequences
Splice sites
5' ss Seq
GTGGTAAGC
5' ss Score
8.15
3' ss Seq
TTGCATTTTCTTTTGTGTAGGGA
3' ss Score
8.06
Exon sequences
Seq C1 exon
GGAGAAGCTGGAGCTGAAGGACCTCCTGGGAAAACTGGCCCGGTCGGACCTCAGGGTCCTTCTGGAAAGCCTGGTCCAGAAGGTCTTCGAGGCATCCCTGGTCCTGTG
Seq A exon
GTAAGCAAGTGTGCTAAAAGGGAATAACTTTACGTTTTAAAACCTATGAATTAAAATGCCTGGAAGGTAGTTGCTTCAAAACTTATAATATGTTCTATGAGCATCCAATTATTAGTATTAAACTTATTTGGTAACTTATTTTAAATAACTTAATAATGTATTTAAAATGCTTATCTTGTTTATTCTATTTATGAAATTCTATGAATTTTAAAATTTATAATTAATTGTATAATTTTGTAGGAACATTCTCATTAGTACAGAAGAGAAAACTAAATTTTAATATGACAGCAATGAAAAGTTTCAAAAATATCTCAGACTATGTCTGTAGATGTTCATGTGCTTATATAAAAATGAGTGCATGCATACATGACTGTATATACATATGTAGGTTCAAAAATTAAAAAATTAAAAAAGTACACTGTTTGTATGTCTTAAGATAGCACAATTTACAGATGCTAATTTTTTTCTTTCTACATGTCCAACATTTAAAAGTAAAAGGTACCCTTCTGTTTGGCAAACAAAGTTGCATTTTCTTTTGTGTAG
Seq C2 exon
GGAGAACAAGGTCTCCCCGGTGCTGCTGGCCAAGATGGACCCCCTGGTCCTCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000023148:ENSRNOT00000068413:56
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=PU(42.1=88.9)
A:
NA
C2:
PF0139113=Collagen=FE(22.4=100),PF0139113=Collagen=PU(6.5=27.8)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]