RnoINT0038851 @ rn6
Intron Retention
Gene
ENSRNOG00000023148 | Col11a1
Description
collagen type XI alpha 1 chain [Source:RGD Symbol;Acc:2372]
Coordinates
chr2:216930648-216931425:+
Coord C1 exon
chr2:216930648-216930764
Coord A exon
chr2:216930765-216931332
Coord C2 exon
chr2:216931333-216931425
Length
568 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAAA
5' ss Score
7.3
3' ss Seq
TCTTCTGAATTTATCATCAGGCA
3' ss Score
6.42
Exon sequences
Seq C1 exon
TATGCACCTGAGGATATAATCGAGTATGACTATGAATATGGGGAGACAGACTATAAAGAGGCTGAGAGTGTAACAGAGATGCCCACTGTCACTGAAGAAACAGTAGCACAAACTGAG
Seq A exon
GTAAAACCAAGAACTGTCTGTTGTATGTGGTGTCCGCTCTTTGTTGTCCTTTAAACTTACCCCACATCTATCACTCGCTTCTGTGAATTAATAACATGTTTTCTTTGACAGAGACCCCTTGCGGGGAGAGCTGACCAGTTTTACATTTTCATTTCCTTTCTTTTTTCCATACGCTTTACTTTCTTTCTCACTCTGTGTTTTCCATTCCGTCTTTCATGACGTTTTACAGAAAAAGAAATCCAATTACACAAAGAAGAAGAGGACATTGGCCACTAACTCAAAGAAAAAATCTAAAATGTCCACAACCCCCAAATCTGAAAAGTTTGCATCCAAGAAGAAGAAACGTAACCAAGCCACAGCCAAAGCCAAACTAGGGGTCCAGGTAGCAAGAAAAAGCTATCAAGATCTGTCCTAGACAAGATGGAAGATCTCTGATGAGTCTTAGTTTTAACCCAATTAGATCAATTCCAATTTGGCTAACACTCTAGTGCAATTAAATCATGATTTTCACTCACTTGAGGTTACATTACAGGTTTCTTAACCCTTGTTCTTCTGAATTTATCATCAG
Seq C2 exon
GCAAATATTGTGGATGACTTTCAAGACTATAACTATGGAACGATGGAAACTTACCAGACTGAGTCTCCTCGGCGGGTATCAGGATCAAATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000023148:ENSRNOT00000068413:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.769 A=NA C2=0.935
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATGCACCTGAGGATATAATCGAGT
R:
ATTTGATCCTGATACCCGCCG
Band lengths:
206-774
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]