RnoINT0038854 @ rn6
Intron Retention
Gene
ENSRNOG00000023148 | Col11a1
Description
collagen type XI alpha 1 chain [Source:RGD Symbol;Acc:2372]
Coordinates
chr2:217042687-217044326:+
Coord C1 exon
chr2:217042687-217042740
Coord A exon
chr2:217042741-217044076
Coord C2 exon
chr2:217044077-217044326
Length
1336 bp
Sequences
Splice sites
5' ss Seq
CCAGTAAGT
5' ss Score
9.09
3' ss Seq
TCACATCAATTTGCTTGCAGGGT
3' ss Score
7.66
Exon sequences
Seq C1 exon
GGACCTACTGGCCAGAAGGGTGACAGTGGTATGCCAGGACCTCCTGGGCCTCCA
Seq A exon
GTAAGTGTATATTAGCAAGAACGATACTTTTTTAACAGGCATATGGGTGCAGGAAATATTTTGTCTGGACTTCTATAACAAGGGGAAGGAATATTCTGCCTAAAGTACTGATTTTGTAGGAAAATCCAACACGGTTCCTCAGGTTATCAACCTACATGTCAAGATTTGTTTTTTAAAGTATCATTTCTTACTTATAAATATTTCTTAATTGTATTCTACAATAAACTAATTAAACTTTCGAGGTAATTATGTACACTTGGGTCACATGTAATGAAACTAATGGAATGAATGCTCACAGAATGAACACACACACAAATATATTTATATGTATTTTTTATTAGCAATGATATTCTTCTGAAGTGTTTGTATTAAACTGTAGACCTATATGTAAGAAATTGTCTTCTGTTTTTCGAGGATATTGTTTTTTTTCCTAGCTAAAGTGTCTCCACTATATGTGTGTTTATTTAGTCCAGTCATAGGGCAAAATACAAGCAGAGTGTCCCTGTGGAAGCTGGAAATCCTAGACCAAACTGTCACAGGTGTGGTTTCTTCTGAAAGGTGTAGGAGGAGAAACTACTTTAAACCTCTCAGATTATACATAACACACTTTTCTTTGATTACCAACCTTGTCTAGATCTGTATCCACGTGACCACATTATTTTTCTTGTCATAAGAATATCAGTGATACTTCACTAGGCCTACCCAAATGACTTCAGCTTACCGAATCATATATTCCACGATCCAAATTGTAAGAAAGTTTGCAATCTGAGTTATTGTGCTGAGGGTCAGAAACAGTAAGTGCATATATAGGCAAAAGATGATTTGACGAGTGAGGATATGAATTAACTGTTTAATGTGGTTGTATGATTACATATCATTAAATTCAACTTATGGAATTTACTTCCAGAGTAATATAGAATAATGTAAGTTATGCATATTTTAATATGTTAATGGGGCAGATCACTTTTTTACTCCTTCAGAAAATAAGCTACTATTGAATAAAGTTTGGATAACCTAAAAGCTTTGTAACATTATATCTAATCATGGATATAGGTATACAAATCAAGATTAGTGAATAAATGAGAGTAACCTATGTAATATGTCGCCAAATTCATACTATGTTAATTTACAGAAAATGTACTAGTAATTATCTGCTTTGCAGACCTGCCTCAATTTCTCTACCATATTTTTCTAAAAATATATCTTTTCATATATGTCATTAATTTAGCAACGGATAGCTAAGCCAATTAATTTCTAAAACGAGTATTACTAGTAAATAAACTCACAGAATACCTTAATCTCTGAAGTAATGACACTCACATCAATTTGCTTGCAG
Seq C2 exon
GGTCCTCCTGGAGAAGTCATACAGCCATTACCTATTTTGTCACCGAAGAAAACAAGAAGACACACTGAAAGCATCCAGGCCGACGCAGGTGATAATATTCTTGACTACTCAGATGGCATGGAGGAAATATTTGGTTCCCTCAATTCTCTGAAACAAGACATTGAACACATGAAGTTTCCCATGGGTACACAGACCAACCCAGCACGAACATGCAAAGACCTGCAGCTCAGCCACCCCGACTTCCCAGATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000023148:ENSRNOT00000068413:62
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=0.845
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(27.0=100)
A:
NA
C2:
PF0139113=Collagen=PD(12.7=9.5),PF0141013=COLFI=PU(12.7=32.1)
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:
TACTGGCCAGAAGGGTGACAG
R:
ATCTGGGAAGTCGGGGTGG
Band lengths:
298-1634
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]