HsaINT0180002 @ hg19
Intron Retention
Gene
ENSG00000038427 | VCAN
Description
versican [Source:HGNC Symbol;Acc:2464]
Coordinates
chr5:82832826-82841469:+
Coord C1 exon
chr5:82832826-82838087
Coord A exon
chr5:82838088-82841355
Coord C2 exon
chr5:82841356-82841469
Length
3268 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
TACTTTCCTGAATATGGTAGGAC
3' ss Score
3.44
Exon sequences
Seq C1 exon
GTCGAATGAGTGATTTGAGTGTAATTGGTCATCCAATAGATTCAGAATCTAAAGAAGATGAACCTTGTAGTGAAGAAACAGATCCAGTGCATGATCTAATGGCTGAAATTTTACCTGAATTCCCTGACATAATTGAAATAGACCTATACCACAGTGAAGAAAATGAAGAAGAAGAAGAAGAGTGTGCAAATGCTACTGATGTGACAACCACCCCATCTGTGCAGTACATAAATGGGAAGCATCTCGTTACCACTGTGCCCAAGGACCCAGAAGCTGCAGAAGCTAGGCGTGGCCAGTTTGAAAGTGTTGCACCTTCTCAGAATTTCTCGGACAGCTCTGAAAGTGATACTCATCCATTTGTAATAGCCAAAACGGAATTGTCTACTGCTGTGCAACCTAATGAATCTACAGAAACAACTGAGTCTCTTGAAGTTACATGGAAGCCTGAGACTTACCCTGAAACATCAGAACATTTTTCAGGTGGTGAGCCTGATGTTTTCCCCACAGTCCCATTCCATGAGGAATTTGAAAGTGGAACAGCCAAAAAAGGGGCAGAATCAGTCACAGAGAGAGATACTGAAGTTGGTCATCAGGCACATGAACATACTGAACCTGTATCTCTGTTTCCTGAAGAGTCTTCAGGAGAGATTGCCATTGACCAAGAATCTCAGAAAATAGCCTTTGCAAGGGCTACAGAAGTAACATTTGGTGAAGAGGTAGAAAAAAGTACTTCTGTCACATACACTCCCACTATAGTTCCAAGTTCTGCATCAGCATATGTTTCAGAGGAAGAAGCAGTTACCCTAATAGGAAATCCTTGGCCAGATGACCTGTTGTCTACCAAAGAAAGCTGGGTAGAAGCAACTCCTAGACAAGTTGTAGAGCTCTCAGGGAGTTCTTCGATTCCAATTACAGAAGGCTCTGGAGAAGCAGAAGAAGATGAAGATACAATGTTCACCATGGTAACTGATTTATCACAGAGAAATACTACTGATACACTCATTACTTTAGACACTAGCAGGATAATCACAGAAAGCTTTTTTGAGGTTCCTGCAACCACCATTTATCCAGTTTCTGAACAACCTTCTGCAAAAGTGGTGCCTACCAAGTTTGTAAGTGAAACAGACACTTCTGAGTGGATTTCCAGTACCACTGTTGAGGAAAAGAAAAGGAAGGAGGAGGAGGGAACTACAGGTACGGCTTCTACATTTGAGGTATATTCATCTACACAGAGATCGGATCAATTAATTTTACCCTTTGAATTAGAAAGTCCAAATGTAGCTACATCTAGTGATTCAGGTACCAGGAAAAGTTTTATGTCCTTGACAACACCAACACAGTCTGAAAGGGAAATGACAGATTCTACTCCTGTCTTTACAGAAACAAATACATTAGAAAATTTGGGGGCACAGACCACTGAGCACAGCAGTATCCATCAACCTGGGGTTCAGGAAGGGCTGACCACTCTCCCACGTAGTCCTGCCTCTGTCTTTATGGAGCAGGGCTCTGGAGAAGCTGCTGCCGACCCAGAAACCACCACTGTTTCTTCATTTTCATTAAACGTAGAGTATGCAATTCAAGCCGAAAAGGAAGTAGCTGGCACTTTGTCTCCGCATGTGGAAACTACATTCTCCACTGAGCCAACAGGACTGGTTTTGAGTACAGTAATGGACAGAGTAGTTGCTGAAAATATAACCCAAACATCCAGGGAAATAGTGATTTCAGAGCGATTAGGAGAACCAAATTATGGGGCAGAAATAAGGGGCTTTTCCACAGGTTTTCCTTTGGAGGAAGATTTCAGTGGTGACTTTAGAGAATACTCAACAGTGTCTCATCCCATAGCAAAAGAAGAAACGGTAATGATGGAAGGCTCTGGAGATGCAGCATTTAGGGACACCCAGACTTCACCATCTACAGTACCTACTTCAGTTCACATCAGTCACATATCTGACTCAGAAGGACCCAGTAGCACCATGGTCAGCACTTCAGCCTTCCCCTGGGAAGAGTTTACATCCTCAGCTGAGGGCTCAGGTGAGCAACTGGTCACAGTCAGCAGCTCTGTTGTTCCAGTGCTTCCCAGTGCTGTGCAAAAGTTTTCTGGTACAGCTTCCTCCATTATCGACGAAGGATTGGGAGAAGTGGGTACTGTCAATGAAATTGATAGAAGATCCACCATTTTACCAACAGCAGAAGTGGAAGGTACGAAAGCTCCAGTAGAGAAGGAGGAAGTAAAGGTCAGTGGCACAGTTTCAACAAACTTTCCCCAAACTATAGAGCCAGCCAAATTATGGTCTAGGCAAGAAGTCAACCCTGTAAGACAAGAAATTGAAAGTGAAACAACATCAGAGGAACAAATTCAAGAAGAAAAGTCATTTGAATCCCCTCAAAACTCTCCTGCAACAGAACAAACAATCTTTGATTCACAGACATTTACTGAAACTGAACTCAAAACCACAGATTATTCTGTACTAACAACAAAGAAAACTTACAGTGATGATAAAGAAATGAAGGAGGAAGACACTTCTTTAGTTAACATGTCTACTCCAGATCCAGATGCAAATGGCTTGGAATCTTACACAACTCTCCCTGAAGCTACTGAAAAGTCACATTTTTTCTTAGCTACTGCATTAGTAACTGAATCTATACCAGCTGAACATGTAGTCACAGATTCACCAATCAAAAAGGAAGAAAGTACAAAACATTTTCCGAAAGGCATGAGACCAACAATTCAAGAGTCAGATACTGAGCTCTTATTCTCTGGACTGGGATCAGGAGAAGAAGTTTTACCTACTCTACCAACAGAGTCAGTGAATTTTACTGAAGTGGAACAAATCAATAACACATTATATCCCCACACTTCTCAAGTGGAAAGTACCTCAAGTGACAAAATTGAAGACTTTAACAGAATGGAAAATGTGGCAAAAGAAGTTGGACCACTCGTATCTCAAACAGACATCTTTGAAGGTAGTGGGTCAGTAACCAGCACAACATTAATAGAAATTTTAAGTGACACTGGAGCAGAAGGACCCACGGTGGCACCTCTCCCTTTCTCCACGGACATCGGACATCCTCAAAATCAGACTGTCAGGTGGGCAGAAGAAATCCAGACTAGTAGACCACAAACCATAACTGAACAAGACTCTAACAAGAATTCTTCAACAGCAGAAATTAACGAAACAACAACCTCATCTACTGATTTTCTGGCTAGAGCTTATGGTTTTGAAATGGCCAAAGAATTTGTTACATCAGCACCAAAACCATCTGACTTGTATTATGAACCTTCTGGAGAAGGATCTGGAGAAGTGGATATTGTTGATTCATTTCACACTTCTGCAACTACTCAGGCAACCAGACAAGAAAGCAGCACCACATTTGTTTCTGATGGGTCCCTGGAAAAACATCCTGAGGTGCCAAGCGCTAAAGCTGTTACTGCTGATGGATTCCCAACAGTTTCAGTGATGCTGCCTCTTCATTCAGAGCAGAACAAAAGCTCCCCTGATCCAACTAGCACACTGTCAAATACAGTGTCATATGAGAGGTCCACAGACGGTAGTTTCCAAGACCGTTTCAGGGAATTCGAGGATTCCACCTTAAAACCTAACAGAAAAAAACCCACTGAAAATATTATCATAGACCTGGACAAAGAGGACAAGGATTTAATATTGACAATTACAGAGAGTACCATCCTTGAAATTCTACCTGAGCTGACATCGGATAAAAATACTATCATAGATATTGATCATACTAAACCTGTGTATGAAGACATTCTTGGAATGCAAACAGATATAGATACAGAGGTACCATCAGAACCACATGACAGTAATGATGAAAGTAATGATGACAGCACTCAAGTTCAAGAGATCTATGAGGCAGCTGTCAACCTTTCTTTAACTGAGGAAACATTTGAGGGCTCTGCTGATGTTCTGGCTAGCTACACTCAGGCAACACATGATGAATCAATGACTTATGAAGATAGAAGCCAACTAGATCACATGGGCTTTCACTTCACAACTGGGATCCCTGCTCCTAGCACAGAAACAGAATTAGACGTTTTACTTCCCACGGCAACATCCCTGCCAATTCCTCGTAAGTCTGCCACAGTTATTCCAGAGATTGAAGGAATAAAAGCTGAAGCAAAAGCCCTGGATGACATGTTTGAATCAAGCACTTTGTCTGATGGTCAAGCTATTGCAGACCAAAGTGAAATAATACCAACATTGGGCCAATTTGAAAGGACTCAGGAGGAGTATGAAGACAAAAAACATGCTGGTCCTTCTTTTCAGCCAGAATTCTCTTCAGGAGCTGAGGAGGCATTAGTAGACCATACTCCCTATCTAAGTATTGCTACTACCCACCTTATGGATCAGAGTGTAACAGAGGTGCCTGATGTGATGGAAGGATCCAATCCCCCATATTACACTGATACAACATTAGCAGTTTCAACATTTGCGAAGTTGTCTTCTCAGACACCATCATCTCCCCTCACTATCTACTCAGGCAGTGAAGCCTCTGGACACACAGAGATCCCCCAGCCCAGTGCTCTGCCAGGAATAGACGTCGGCTCATCTGTAATGTCCCCACAGGATTCTTTTAAGGAAATTCATGTAAATATTGAAGCGACTTTCAAACCATCAAGTGAGGAATACCTTCACATAACTGAGCCTCCCTCTTTATCTCCTGACACAAAATTAGAACCTTCAGAAGATGATGGTAAACCTGAGTTATTAGAAGAAATGGAAGCTTCTCCCACAGAACTTATTGCTGTGGAAGGAACTGAGATTCTCCAAGATTTCCAAAACAAAACCGATGGTCAAGTTTCTGGAGAAGCAATCAAGATGTTTCCCACCATTAAAACACCTGAGGCTGGAACTGTTATTACAACTGCCGATGAAATTGAATTAGAAGGTGCTACACAGTGGCCACACTCTACTTCTGCTTCTGCCACCTATGGGGTCGAGGCAGGTGTGGTGCCTTGGCTAAGTCCACAGACTTCTGAGAGGCCCACGCTTTCTTCTTCTCCAGAAATAAACCCTGAAACTCAAGCAGCTTTAATCAGAGGGCAGGATTCCACGATAGCAGCATCAGAACAGCAAGTGGCAGCGAGAATTCTTGATTCCAATGATCAGGCAACAGTAAACCCTGTGGAATTTAATACTGAGGTTGCAACACCACCATTTTCCCTTCTGGAGACTTCTAATGAAACAGATTTCCTGATTGGCATTAATGAAGAGTCAGTGGAAGGCACGGCAATCTATTTACCAG
Seq A exon
GTAAGATCACAACATTGATAAATCTGTTTCCAAACCTGGAAACAGTCCCTTGGTGCTAACGTTTATATGTATGTAATTTTTATTGTGATGTTAAATCAATGGAGAGTTTCATATTATTCACATAACAGCAGGCCAGGCCACAGTATTGAGTTCATAATGAGATGAAATGACAGTAAGTATAGATTAGTTTTGGACTTTAGAAGTAGACTTTGTATTTTTCTGGGTTTTAGAAATAATATACAATTACAACATGGAAAAGATGAAATTATTAATGTTATAAAAATTCAATTTGTTTTTACTCACAACTAGAGTATTGCTTTGTCATATGTCTCATAGTTATACATGTTAGGTTTAAAAGTAGAAAAAAAGTCCTATTTTTAAAAACCCTCCCATTGATGGATGCTATTGCTGTAGTATCAAAATCTGTCAGGCCTTTAACATTTGGGAGTAGTACGTAGCTCTAATAATTATTTCAGAGTTTGTGCAGTATCAATATCAGCTCATACTTATATGCAATGTCCTTGTTTAAGACAGTCTACATAATGCATCAAACACAGTGCCTACCAGTAGTGAGTAGTCATTTATTATATAAACATACTGCCTGTTGAGAGAAGTTTTCTGTGTATTTACTGAATGTATGGAAAGCATGAATTTGATACTGATTCATATAAGCCATCTCTTCTGATTGCCACGAAAAGGCTATAAAAGCCCTGTGTGAAAGGGTAAGAGGTGAAGGTTCAGAGAGGTTCAGCAACTTGCCCAAGGTGGCACAGCCACATTGTGGTAAAAGTAGGATTTGAACCCAGCTTAGCTCCACTCTAAAGTCCATAGTCTTTTCACTGCTCTTTGCTGGTTTCAGTATAGTATAAAAATAAACAATTGATATTGAATAATATATGAACCAGGAATCTTGGAATATTTACTTTGTAGAATTTATTTTCCTCTTAATCTAGCCTGAGAATGTTAAGAAATCAGCTCTAATGGTGTTTTCCCATAATGTTATTATTTAAATTAACAATGTCAGTGGAATCCACAAATAGACATCACCACCTAGCTGCTACCTGCAAAAAGAGGAAGAAAAATCAGTACTTTAATGTCTGTCTTGGTTGAGAATATATGTTTTATTTTAATATGTTTTATGCCATGACTATCGTTAAAATTATTCTTCTGATCATATCAATATTACCTTTTGTGCCACCAATGCTTTATTTTGATGTGCTTCAGAAAGAGTAAAATAGAAAGTACAATTTTTAATAAATGGCTTGAAATATTTTGAGGAAAATTGATCAAAGGTAGTTGACATTGGGTTTTTTGTTATCACTGTGTGTTAAATCTGTAAATGATAATCTAGTAATTTGGCTAATATTTATTGTTTTTTAATTTAGTTTAATATACTTCAGTTTGTTAAAAATATGATGTAAAAATAACTGGTAATAACTAGGTACATATAGAGTTAAGTTTGATGAATGAGAAATATGTACCAATTTTCCAGTTTACAATATTTACCAAGATTTATAGTTTGCGTCTTCATTGCAAAACAAATGGTCACTTTAGCTTAATTCAGTAAACAGCAGCTCATATGGGATTACCTGGTCTATCTGTTGCAGATTCAACTTTCAGAGGTTAATACGAACTGTTTAGGGGAGAATAACATTCATAAAAACTGAAGTTTCCTGTTAATTGGAACGACTTCCAGTTCACAGGAAGACTCACTCACTCAGTCCTTGTTTCATGGTCTCAGCATGGTGTCTAGTGTCAGTGGTAGGAATAGTAATAGTACTTCTTCACATTTGTGTGGCACATCACAGTCTGATAAAGCACTTTCACCTAGTGTCATTTGGATTCAGCACAGAGGGCAGCATGTGGCTATGGCGTGTGTTAACTGCAGCCTTGTCATCCTGGCAGCGAGCGTACTTGTACTTTAAAATTCAGAAAGCTAAAATTGTTAGGGAGATTTCAAATAGTTTTGGAACTATAGGAAAAAGTGTCTTAGAAAACTCGGGGGAGTTTTTGGAGAAGTTGATGTACTCATCTGAATTAACCTAATTTTAACGTGAATCCCAAACATGGGAATGTGTACCTATCCAGGTTTATAGTCATTCAGAATTTACTTAACACTCAGAAAGTTTGAGTTTGACTTTCTGGTGTGGGGAAGTCTCAGTTATCTTTTATAGCAGTACCTTGTTTATCCTGATATTCTTTAAGCTAATGTTTCATAAGAAGTTAGACATCTTTCTTCTTTCATGTGTAATTATTTCAGGGTTTCAGGACTTAAGATTCTTGAAAGTATGGGTGTATTCCATAGATAATCTATTTTATTTCAATTATTTTGTAAAACTTTCAACTCTCATTTGGATCTTTGAAGATTTAGAAATGTAAGCAAGTCTGAAACAATATACAAAGAATAAGTATAAACTCAATGAAAATACACTTATCCAAGCAATATTGCAATATAAAATATATGCTTCAAGTGGTGTAAAAGTGTTTGCACTTAGAAAATATATTTAAACTGTTTGTCCTCATAAATTTATGTCTTCGGCCTTCATATTTATCTCCCAGGAGTGTCGGTTTTATTTGTATTTTAATAAGAAAATTATAATAAAAACTTGGGGTTTCATTTTAGGTGAGGTTTTTGTATTTGGGTTTGTTTTTCTACAGTAGAGTTTAATCCATGTGTTGCTTTTCTTCAAGTATAGTTTAAAGGAGTACATTTGGAACGTGTTTTTGGAAAAAGCATGTTAATGTAGCAGAAGAGACTTCAGTGCACACTTTCGAAGAAAAACAGTTTCTGAGCATTAAGTGGTAAAAGGCAATAATAATTCAAATGATGATAACAAGCCAACCTGCTAAAAAGAATGCATGTTCTGTGTATCCAGCCATTTCACATGAACTAACCCCATTTAAAAGAATACATTTTCCATTCACTGTGCACATATGTGTAATCATTTTTGACTAAAATCAATTGCCATTATCATGCCAACTAAATCTGCAGTAGAATATATTAGTTGCCAGATACAGTACAAAAAATATCATTTAAGAGTAATCGTGATTGAATCCCAGAAATGAATAGATGCAATTTGTAACAATTAGTTATAATGCCAAGAAACACTCCAGAGAGTAAAGTTAATGTTAATTTTTATATGTAGTAACTCTAAATTGCTATGGTAAAGCCTATAATATGGTAGCAATATGGGGCGTTTTATGCTAAAATACACGCAAACATTAGAGACGAGCCTAACTGCTTTTCTTACTTTCCTGAATATGGTAG
Seq C2 exon
GACCTGATCGCTGCAAAATGAACCCGTGCCTTAACGGAGGCACCTGTTATCCTACTGAAACTTCCTACGTATGCACCTGTGTGCCAGGATACAGCGGAGACCAGTGTGAACTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000038427-VCAN:NM_001164097:7
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.780 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
Rat
(rn6)
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]
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)