RnoINT0038824 @ rn6
Intron Retention
Gene
ENSRNOG00000023148 | Col11a1
Description
collagen type XI alpha 1 chain [Source:RGD Symbol;Acc:2372]
Coordinates
chr2:216979266-216983989:+
Coord C1 exon
chr2:216979266-216979310
Coord A exon
chr2:216979311-216983935
Coord C2 exon
chr2:216983936-216983989
Length
4625 bp
Sequences
Splice sites
5' ss Seq
AGGGTACGT
5' ss Score
9.15
3' ss Seq
TAACGTTTATGTGTTTTCAGGGC
3' ss Score
8.96
Exon sequences
Seq C1 exon
GGTACATCAGGTGGTGATGGCCCTCCTGGCCCACCAGGCGAAAGG
Seq A exon
GTACGTATAGCACAGTCACATGAGGCACAATGAAAATGAATGCTTTAATAAATATTTAGATTCTACAAGAGGGTACATAAGTCTACAAGACACATTCATCTACCGTTTCTTACTTTTTATAATTCCTTTCCCCTGCCAACTTAAAACTTGCTAGGCCAGGGGCAAACAATTTTTATAAAAATTAGAAAAATAACGTGTATAATAGGCTGAAGGTAGAACATGCCAATAAAAATAGAGATTTTATTTGAAATATACTTTGGTTCCCATGCTTTCCCCTGAGTTGCATGTTTGTGGTCAATTTGTCTCTGGAGCTGGCAATAACATGATGTTGGTAAAATGCAAGTACCAGTAGCCATTAAGTCATGATCAATATCACATTCAAGTCAAGATAAAACATCTATTCCAGTAAATAAAAAAACTATTTAGTAAATTGATTTTCAGTTGATATGAAGTAAAGCCAAATACAGCTGAACAACCAGGACCTTGGTTTGAGTGCTTTGGCAAGAGAGAGCATTATTAGAGCAATGTTATTTGAAAGCCATCGCCTTGCAAGAATTTTGAATTTAAAAATTTATAGCACATCAAAAAGTATTGTAATCTGTCTTAGTTTTATATTTTATTTTTTTGACTATTTTTTGTTTACACTTCAAATGTTATTCCCCTTCCCAGTTTCACCTCTACAAACCCCATCCCGTCTCCCTGCTTCTACGCGGATGCTCCCCCACCCATTCACCCACTCCCACTTCAGCAACCTAGAATTCTCCTACACTGGGTCTTAGTTTTATATAGTAACTTCATGTATTATTAAATTAAGCTGATGTCATTTTATAGGTATTTCGGGTGTAAGATGTACAATTATGTGTGAGTCCATGGGCATCAGTGTGTGTGAATGAGAGTTCATGCGTGATATTAGAGGATAACCTCTGAGATGATTTCTGGCTTTCTACCTTTTTTTTGAGTCATTTTCTCGTTACTGTTATTCTGCTCTGTGTGCTGTCTTATTTGGCTTAGGAGAGTCCAAAGATTCATCTGCCTGTGCTTTCCGTCTCCCCAGGGAATACTGAGATTACACATGCAGACTCAGGTGTTAAGCTTTTTATAAGGGGTTGTGTGGCTCAAACAGAAGTCTTTCTGTTTGTGCCATCTTCCCAGCACACATTTTCTCCATTTTCATTTGTAACTTGAAGGTTGATATGCCACATATGAAAAATGGAAACACCTATGATGGATAACAGTAAACTGATCATGAGAATTTGAGTTTCTAAACCAAAGGTGAAGTGAAATTTAGGTTCCGTTTGTAACAAAATTAAAAGAAAAGAGTAAGCATTTAATTAAAGTTTCTTTATGGTCTAGTTCATATTTAATTAAATTACTCACTACATGTTTTTCTCTCCACATGAATTATTTCCAAATTAAGTGGATTCCTCTCACACATTTTGAATTCATAAATAATGTATATATTTGATATATTTGATGGTTCAAGTAATGGTCGTAAAAAGATATATTTACTTTAAATGGATGAATCATTAAATTAATAGAACAGTTTAACAAGTCATGTAACGACCAAGTTTTATTATGCTTTAAAGCACCAATGAAAGTGCATCTTGATTTGCAAAATAGCATGACTAGGCAACGTGAGTACTTTCAGAAAGACATCAGCGACAGTGTACATTTTGAAGATAAGAATGAAGGGTTTGGGGGCTTGGGATTTAGCTCAGTGGTAGAGCGCTTACCTAGGAAGCGCAAGGCCCTGGGTTCGGTCCCCAGCTCCGAAAAAAAGAACCAAAAAAAAAAAAAGAATGAAGGGTTTGTTTGTTTCTTTGTTTTGCTTTTTCTTTATTTGTAACCTAGAATGACTTATTCCTAATAAAGTTATTGAATCATTCAGGTTGTACATAGGGAGAAAATAGCATTGCTACAGTATGTGGTAAATGCCACCTATATTCATATTCTCTCCCCCGTTTTCTGGCAGGAACTTTAAATATGTTTCACTCGTTTATGTATGTGTTTTTTAAATTAGTTTTTAATTAGCATATAAAAGATCTATTTATGACATTTTAAAACATAGTTTGTTTTTGCTGACCTAAGGTTTTTTTACCTCATCTCCTGTTTTTCATCTGGTTGGTCCCAAGTGGCCGGTCCTGCATACATATACAGACAAGTAACACTAAATGGGCTATAACAAGTAAATAGGTTGTGTGCATGTGTGTTTGTGTGTGCATCTGGGCATTACTGGTTATTAGTTGTTATAAGCTTGAAATGGACTGTGGGAAATGTGAGAAGTTGAAGAAGGAATAGAAAGGGCAAAATATTGGAATTACATTAATCATGTATGACTTACAAATAATTATCAACTAAATAAAATCTTAGTTTTACAATGAATTTTTTTAAATGTTTAAGTTCTCATGTAGATTTTGAAGAATAGTGGTTTCATGTTTTAAGAGGGTAAATTATTAATTCTTAATACTCGTTCATTGGAGATTTGAGACCATTATTTTTTCTTCTATATTTATTTATTTATTTATTCATTTAATCATTTTATTTCTTTACATTCCATAAGTTCCCCCTTCCCAGTTCCCTTCCCATAGTTCCTCATCCTTTAGCTTTTGATTATAATATAGATGCTATAAATATCAAAGGCTTATATTTATTTGTAATGTAGCATTGGATTAAAATGCTAGTGAAAGTCTTTTTGTGACGACATAACTGATAGCATAAAAACTAAAGTACCCTGAGCACCTCCTTCAGTAAGCTGTTTTCTTGCTTTGCAAACAGTAAGTTTAACACTCATCTTATTACACAAGACATTTTATATTGATTATGTCCCATTTTGTATGTCTTCATTTCATAGATATAAATCATGTCCTTGGCAAGTCTAGGCTTAACTTTTAGCAATCCATTTTCTTGATACCAAAACAATCTCTATAACTGAATGGACTTTATGCATTTTAGAGATGTGCAAATAAGAACCTGAATGATATAACTAATTCCATATCAAGCTAGGAGTGGTATTATAAATACCTCGTAGGGTAGCATGTTAATAAGAATAATTGCAGAGTTCATCTTGTCTTGTGTACTAAATAGTGTAATGCAGAGAACAACACTGACAAATGACAGAATTATTGCCCCAGCGTGTTTGCTAGGGCTAAGCGTACCACAATGCTTTAGTAATGATCATGTATGCTTCCTGTTATCTGTATATTACTAGACTCAGAATTATTTTGGAGTGCATTGGAGTTTTCAGTTTGGAGGTTGATTGAAACTTCATTTAATATCTCTCTTTATAAATGCTTGCAACCAACATTAAAAGAATATGCACTGTGAAACTTCTCAGAGAGATGGACATGCTCTATTGCTTTGTTAATTATATTTGATTACTTAAATTTGTTCTTTGACACGTTTCATATATGTGCATAAGGCATACTGACCATTCTCCCATAGCACTCCTCCCAACTTCATCCCACCACTGTTTATCACCCCATCTCTTCAAATTCCAGTCTCACTTTCATGTCTGTGCTTCCTTTGTCACCCACTGTGATGAACTAGCACATCTATGTGAAACTTGGTTTATAGCTGTCTCTTAGCACTTGTTGGAACCAGCAGGGGTTACAGTATAAAGAGTGTGAATTCCAATCCCACAGATTCTCTCAGTAGCTCATAGTTCAGTAACAAGCCACCTCATGACTTTCATGACTGACTGTTGATAAGGCCAGTATTGTATATGCCAACTGAGGTGACCATACTTGCGTGTAAAATTTGTGATGAGTCTACCTCCTGTTCTCTCTTCCTCAGTATCCCCCAGTCTTCGAACCGGATGTATATATACATCTTGTGTAGGAATATTAGCATTTTATACAAACAGTAAATATTCACAGTTCTCTTGAAATAATGTTGGTGTGTTGTGCAGTTTCTCATAGTTAGATGGCCCCACCCGGGATTCCATCCCATATACTGTCACCAAACCCAGACAATATTGTTGATTCCAAGAAATGTATGCTAACAGGAGCCTGTTATAGCTGTCTCAAAATCAGATGCTCTCAACCAACCATTGGAATGCAAACGGGATCCCCAATGGAGGAGTTAGAAAAAGGACTGAAGGAGCTGAAGGGGTTCCCAACTCCTAGGAAGAACAATATAAACCAACCAGACGCCCCCCAGAGCTCTCAGAGACTAAACCACCAACCAAAGAGTACACATGGAGGGACCCATGGCTCCAGCCACATATATAGCAGAGCCTTGGGCATCAGTAAGAGGAGAGGCTGTTGACCCTGTGAAGGCTTAATGCCCCAGTGTAGCGTAAAGTCAGGGCAGGAGATGGGAGGGAGTGGGTGGATGGGTGAGAGAACACCCTCATAGAGGCAGGGGGCTGGGAGAAGCCAGGAAAGGGGATAACATTTAAAATGTAAGGAAAGAAAATGTACAATAGAAAAAAAATAAAACAAACAAAAAAATTAAATCATTTCAGTTCTAAGCTAGACTGGTCAAAATATTATATTTCCACGCTTTCATAACTAAAATGGGGAAATTCATGAGTGTTTTGTTTGACCAAGTGAACTACAAAAGACATAAAGACATACCCTTGAAGATTTATTGTTAAATTTTCTTTAACGTTTATGTGTTTTCAG
Seq C2 exon
GGCCCTCAAGGACCTCAAGGTCCAGTTGGATTCCCTGGACCAAAAGGCCCCCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000023148:ENSRNOT00000068413:35
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.750 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:
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]