RnoINT0162711 @ rn6
Intron Retention
Gene
ENSRNOG00000029212 | Vcan
Description
versican [Source:RGD Symbol;Acc:619940]
Coordinates
chr2:18522562-18528935:-
Coord C1 exon
chr2:18525795-18528935
Coord A exon
chr2:18522676-18525794
Coord C2 exon
chr2:18522562-18522675
Length
3119 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
TATTTTCCTGAATGTGCTAGGAC
3' ss Score
5.27
Exon sequences
Seq C1 exon
GTGTGGACATTCTTCCTACTACAGAGTCTCCATATTTTGATCAAGAGTTTGAAGAAGCGGCTGCAGTGACAGAAGCAGGTAAACAATCTGCTTTGCCAATAGCAGTGAGTGGAAATACTGTAGATCTGACAGAAAACAGGGACATAGAGGTAAACAGCACAATGTCAGTAGACCTTCCCCAGACAATGGAGCCAGCCAAATTATGGTCTAAACCAGAAGTCAATCCTGAAAAACAAGAGATTGGAAGCGAAACAGTGACACAGGATAAAGCTCAGGGACAAAAGTCTTTTGAATCGCTCCACAGTTCTCTTGCACCAGAACAAACAACTTTGGAAAGCCAATCACTTATTGAAACTGAAGTCCAAACTTCATATTACTCTATGTTAACAACAATGAAAACATACAATACTAATGAGGAAGTGGAGGAGGAAGGCACGTCCATAGCTCATATGTCTACTCCAGGCCCGGGAATCAAAGGCTTGGAATCATATCCTACCCATCCTGAAGCTACTGGGAAGTCATACTCTTTCTCAGCTTCTGCCTTAGTGACTGAATCTGGACCAGCTAGAAGTGTAGTCATGGATTCCTCAACTCAAGAGGAAGAAAGTATAAAACTCTTCCAAAAGGACATGATACTAACACATAAAGAGTCAAATTCTGATCTCTCGTTCTCTGGCCTGGGATCAGGAGAGGCTTTGCCTCCTCTCCCTACAACATCAGTGAGTTTGACTGACATGGGAAAGATCAATAGCACATTGTATCCTGAGACATCTCACATGGAAAGCTTAGGAACAAGCATCTTAGGAGATAACCATGAAAGAATGAAAAATGTGTCAAATGAAGTTAGAACCCTTATTTCCGAAACAGGCAGCATTTCTCAAGACAGTACGGAGGCACCCAATACAACTTTGAGTGATACCAGAACAGAAGAATCTACAACTTCACCTCTTCCTTTCATGAAGCTCATGGACACGGAACATTCTCCAAAGCAGACCCTCAGGTGGGAAGAGGAAATCCAGACCCATAGGCCACAAACTATGACTGGACAGATTACCAATGACAATTCTTCAGTGTCAGAAGCTGAAGCAGCAGCAACCTCTGCCCCTGCTTTTCTGCCTGAAACCTACAGTGTTGAAATGACCAAAGCCTTTGCTACATCACTGTCACAAACATCTGACTTGTTTGATGCAAATTCTGGAGAAGGATCTGGAGAAGTGGATGGTCTTGACTTAGTGTACACTTCTAGAACTACTCAGGCAAGCAGTCAAGGAGACAGCATGTTTGCCTCTCATGGATTCATTGAAAAGCATCCAGAGGTGTCAAGGACCGAGACTGGAGCTACTGATGGATCTCCAACAGCTTCAGCGATGTTCCTGCATCAGTCAGAGTACAATGAGAGTTCCCTGTATCCAACCAGCACACTGCCAAGCACAGTGACATATGAGAGTCCCTCAGAAGGTATTGCAGATGGTTTGCAAGACCATATCAGATTCGAAGTTTCTACCTTGAAACCTAGCAGAAGGAAAGCCACTGAGAGCGTTATTATAGATTTAGACAAAGAGGATAGTAAGGACTTAGGGTTGGCAATTACTGAGAGTGCTATTGTTGAAATTCTCCCTGAGCTGACATCAGATAGAAATATTATTATAGACATTGATCACACTAAACCTGTATATGAGTACATCCCTGGAATACAAACAGACCTAGATTCAGACATACCATTGGGATCACATGGCAGTAGTGAAGAAAGCCTTGAAGTTCAAGAGAAGTATGAAGCAACTATTAACCTGTCTCCAACTGAGGAAGCATTTGACGGCTCTGGTGATGCACTTCCTGCTGGTCACACTCAAGCGATATACAATGAGTCTGTGACTCCCAGTGATGGAAAGCAGCCAGAGGACATAAGCTTTAGTTTTGCAACTGGAATCCCAGTTTCTAGCACAGAGACAGAATTAAATACTTTCTTCCCTACAGTGTCAACCCTGCACATTCCTAGCAAACTAACCACCGCTAGTCCAGAGATTGATAAACCCAACATTGAAGCAATATCACTGGATGATATATTTGAATCAAGCACCTTGTCTGATGGCCAAGCTATTGCCGATCAGAGTGAAGTAATATCAACACTAGGCCATTTGGAAAAGACACAGGAAGAGTATGAAGAAAAGAAATATGGAGGTCCTTCTTTTCAGCCAGAATTCTTTTCAGGAGTGGGTGAAGTATTCACAGATGCCCCTGCTTATGTAAGTATTGGTAGGACATACTCTGTAGCTCAGCCTTTAACAGAATTCCCCAATGTGGTAGGACAATCTGACTCCACACATTACACTGAAGCAACATCTGCAGTTTCCTCTGTGACAGAGCTGTCTCCTCAGACACCATCTTCTCCCTCTCCTGTCTACATAGACAGTGGAGTCTCTGAATTCACAGAGGTCCCCCACAAAAGTGCTCAGCCAGCTCCTACTGCCGCTTCATCACAAAAGTTGATAGAGGGTTCTTTTAAGGAAGTGCGTGCTAATATTGAAGCTACCATCAAGTCGCTGGGTGAAAATGATCACGGAACAGAGTCTCCATCCATGTCTCCTAGCCCTGCTTTAGACATTTCAGAAGACGACAGTAAACCTAAGTTACTAGAAGACCTGGAAACTTCTCCCACAAAAACCGAGACTTCCCAAGATTCCCCAAACAAAGCAAATGATCAAATTCCAGGAAAAACAGCTGGAATCCTTGCTGGTATCAAAACAACAGAGAGTGGACCAGTCGTTACAGCTGCAGATGACATGGAGCTAGGAGATGCCACACAGCGGCCACATTCTGCTTCTGCTCCTGCAGCTTTCAGGGTTGAGACAAGTATGGTACCTCAGCCCATCCCACAGGAGCCTGAGAGGCCAACCTTTCCTTCCCTGGAAATTAACCATGAAACACACACATCATTATTTGAAGAATCTATATTGGCAACATCTGAAAAACAAGTGTCCCAAAGAATTCTTGATTACAGTAACCAGGCAACAGTCAGTACTCTGGATCTAAATACTGAACACTCAATACCACCATTTTCCATTCTGGACAATTCTAACGAAACTGCTTTCCTGATTGGCATTAGTGAAGAGACCGTGGAAGGCACAGCAGTTTATCTACCAG
Seq A exon
GTAAGATGTCAACATTGCTACATCTGTTTCCAAGGCTGGGATGAGCCCCTTGGTTCTATATATCTGTGTATGCCTTTTATTGTAATGTGAAATTCATAGCCACTTTTATATTGTTCAGGCCAAGCCACAGTAGAGAGTCATAAGTCAATGCAATGAATGTAAGTATGGGCACTTCTGAACTTTACAGATGTCCTTTGCTTCCCCCACGCCCCTGCGTCTTACAGACAACATACAGTTGTAACATGGATAAAGTGAAATAATAATCTAAAACTCGTGTGTTTTCATCTACAGCTGAAATATTGCCTTGTTGTAGGTCCTACAATACATGCCATAGCTGTGAAAATGGGGAAAAAAAATCACACTTTTCTTTTAACCCTCCCCCCATTTAAGAGATGTTCTTATGACAGCACCGAAATCTGTTAGGCCTTTAAGTTTTGAGAATAGTAAGTGTTTCTTACAAATGCCTTGTGGTCAGTTGTTCCTCCAGTTACCATTTGTACTCTAGTGTGATGTGATGCCCTTGCTGGAAACAGTTTATACAATTCTGCTGACTCAGCTCCTAGTCATAGTGTATTTAGTATGTTTACATTCTACCTCTTGAAAAATTAATTTCTATTTATTTACTGACTATAAAAAGCATAGAATTGGTACTACTTCATATAGACCATTTCATTTAATCTTCACGAAATGTCTAAATGCTCATCCTTTTACATTAGCTCAATGTAAAAGGATAAGACATAGGTATTCAGAAAGGGCCAGTAATTTGCCCAAGGATGCACAGCCATACCATGGCAGAAATGGTGTTTTAATCCAAAACAGCCCTAATCTGACGTCCATGGTCTTTTTACTGCCCTTTTACTGGTTTTCAATATAGCGTAAAACTAACGACTGGTATTTAATAATATATAGACAATAAACTTGAAATTTTTATTTAGTAGAGGTGACATTTTTCTTAATCTAAGTTTTTTAGTCTGTTCCTGGAATGCTATTATTTAAATAGGAATAATAATGGAACCCACCAGTAACCGTCATCATTTAATGACTTCCTAGAAAAGGAAAGAAAGCAAGAAAGGAAGGGAAGAGAGGAAGGAGAGACGGAGGGAGGGAAGGAGGATCAATATTAAGGACTGTCTTGGTTAGAAATACGTTTTAGCTTAAATACTGTACTTTAGGTCATGGCTATTAAAATTATTCTTCTAGTCTTACTAATATTACCGGGACACATGTTTTACCTTGGGAAACAGAAGAATAGCTTTATTTAAAGCTTGAGATTTTAATAAAATAGTAAGAGTTTAATAAAATGATAACAGAGTATTTTGTGCTCCAAGGTGGTTGACACTGGGGATATGTTGGGGATACAATAAATATATAATTATCACCTAGTCATCTGGCCCATATTTATTGTTTTACCATTAAGTTGAAACGCACTTAAGAATATGGAAATAATTGACAGAGGATGGGGAACCATATCTGTGCGGTTCAGACTCCAGGACAGCGTTCTCAGTAGTAAGTAGTCAATCGTAGTAAGGACTATTTCTAATTCAGGAGGCAGCCTCCTGTGTGGGGGCCTGGCCTATCTGCTGCAGGTTTAGCTTTCTCAGGTCCACCCAAACTACTCGGGCAAGAACAATGTGCTAAAAAGGCAAGCCCGTCTCTTAATCAGAACTGCTTTGAGTTCACAGAAAAAGCTCTTTTCCTGCCCATACCTGTCACCTGAACTCAATGTGGTACCTGGTGTCTATGATGGGGGTGAAAGCAGTCACAGTACCATAGGCTCGGCCACCTAAGTGTCCGTTGGATTCCATTTAGTGTCCGCATGTCACAGATTACAACCTTGTCACCGAGGCAATATGTGGAAAACCAAGTGTTAGGGAGGTTTTAAGAATCTTTGGAAATGCAAGAGAAAGTATTTTTAGAAAAAATCAAGGCAGATTTTAGAGAAACTGAAGTATATATCTGGGTTTTCCTGATTTTAATATGAACTAAAAATGGATGTGTAGATTCATCAGGCCCATCTAGTTGTCCAGATTTCACCCAATGCTATAAAGGTTGGCTTTGAACTTCTTGTCTGAGATCTTCACGTTTCTTCTATAGCCAATGTTTCACCAGATATTAGATATTTCTTCATGTGCATGTATTTCAGATTTAGGATTTATACGATTTTTGAAACTGCAATTGTATACACATAGCATCTATGTAATTTAAATTGTTTTGCAAAACTTCCAAGTTTCACTTGGATCCCTGGACAATTTGGGAATTAAACATCTCTAAAATAATACTCAAGTTCTCCATAATATTCATATATCTAGACAATGTTATGAAATAAAATATATGTTTCAGAGGTGTAAAGTATTTATATTTAAAAAATCCCTTAAATTATTATATTAAACTGAAAATTTCCGGTTTGAGCTTTGCATCGATCTCTAGGAGGGTTAGTTTTATTTATGTTTTATTACGAAAGTTGAATAAAATTTGGGGCTTCATTTTGAGTGAGCTTTTGTATTTGGAGTTGTTTTCATACCATAGAGTTTAATCCATGTGTTGCTTTTCTTCAAGTATAGTTTAAAGGAGTACAGTTGGAACGTGTTTTTGGAAAAGGCATGTTAATGTAGCAGAAGAAACGTCAGTGCACACTTTCGAAGACAGTTTCTGAGCATTAAGTGGTAAAAGGCAATAGTAATTCAAGCACTGGTAACAAGCCAATATGCTAAAAGAATGCATGTTCTGTGTACTCAGCCATTTCACATGAACTAACATCGTTTAAAACAATACATTTCCATTCACTGTGCACATATGTGTAATCATTTTTAACTAAAATCAAATGCCATTATCATGCCAATTAATCTGCCATAGAAAAACGTTAGCTGCCAGATGTGGTATAACGTACTGTTTACAAGTAGTAACGATTGAATCCTAGCAATGAATAGAAGGGATTTGTAACAATTGGTTATAATGCCAAGGAACACTCCAGAGTAAAGTTAATTTTATATCCATATAGTATCTTTATAAATTGCTATGGTAAAGCTTATGTTGTGGTAGCAGGAAGAGACATTTTGTGCTAAAATATAGTCAGACCTAGGAGAAACGGCTAATTGTCCTTATTTTCCTGAATGTGCTAG
Seq C2 exon
GACCTGATCTCTGCAAAACAAACCCATGCCTCAATGGAGGCACCTGCTATCCTACTGAGACTTCCTATGTGTGCACCTGTGCACCTGGCTACAGTGGAGACCAGTGTGAACTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000029212:ENSRNOT00000045532:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.737 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0000822=EGF=WD(100=79.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
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]