RnoINT0011753 @ rn6
Intron Retention
Gene
ENSRNOG00000028992 | Acan
Description
aggrecan [Source:RGD Symbol;Acc:68358]
Coordinates
chr1:140794427-140796367:+
Coord C1 exon
chr1:140794427-140794810
Coord A exon
chr1:140794811-140796192
Coord C2 exon
chr1:140796193-140796367
Length
1382 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAAG
5' ss Score
5.73
3' ss Seq
CTGGTCCATGTGTCCTACAGGCA
3' ss Score
8.65
Exon sequences
Seq C1 exon
ACCATGACAACTCACTGAGTGTGAGCATCCCTCAACCATCCCCACTGAAGGCCCTCCTAGGGACTTCCCTCACCATCCCCTGCTACTTCATCGACCCCATGCATCCTGTGACCACTGCTCCCTCCACTGCCCCCCTCACCCCAAGAATCAAGTGGAGCCGTGTTTCCAAGGAAAAGGAGGTGGTACTGTTGGTGGCCACTGAAGGACAGGTTCGAGTGAACAGCATCTACCAAGACAAGGTGTCACTTCCCAACTATCCAGCCATCCCCAGCGATGCCACCTTGGAAATCCAGAACCTTCGCTCCAATGACTCTGGGATCTATCGGTGTGAAGTGATGCATGGCATTGAGGACAGCGAAGCCACCCTGGAGGTCATAGTAAAAG
Seq A exon
GTGAAGGGCCTCCCATTGGGCCGCCATGCTGCCTGTAGAAAGAACTAGAATGATGTCCCCAGCAGTGTGGGCCTTGGTGACTAGCTCTCCCACTCACTCGCCCCTCTGCATGCTCATTTTCTCTTTATTTTCCCCTAATGTGAGACTGACTGGCAAATGCTGTTCTCTGTGGGATTGGGACTCCAGGAGTGGGACAGGTAAATAATCCTGGTATTGGCAGCTTGTTTGCCAGCAATCACTCACTTGTTGGGTGTATCTGCTTTTCTCATTGCTGTGATTGAATGCCTTACAGGAGTCCACTTGAGGGAGGGAGGCATTACCCTGGCTCACAGTTTGAAGGGATACAGCCAACCGTGGTGGGGCAAGATGGCAGCAGAAGTGTGAGGCAGATAATCACACTGCATCAACAGTCAGAAGGAAGTGCTCACCCAGATTACTTTCTCCTTCTTTCTTTTTTTCACTCTGGGACCCTGAACTGTGTGATGGCACCACCTACCTTCAGGGTAGGCCTTCCCTCTTCAGTTAAACCCTCACAGACATACCCAGAGGTGTGTCTTCTACCTTTTAGCAGGCTTTGTAAGTGTGCCCATTTTGCACCTAAGTAAATGAGTTGCTAGCATGTCTGCTGTGACCCTAGAAATGAGGGAAAGTGGGTTCCTAAAACGTCATTCATCTAGGTATCTCCCCCCTCTCCACCCTTTATTCTCAGCTTTGGAGACCAAAGAAATGACTGATGATTCACTTCCTCATCGCCTTTGTCTCTAAGAGGTCTGGTTAGGATGCCACTGAGCTAGGGCAGGGGAGATTAGAGGGTCCTGGAGTGACCAAAAGAAAATCACAAGGAGACAGTTTTTGCCTTAGTTCCAATAACTTTCTTACTGTCAGGATTATTATAGGTGTTTTAAAATGAACGCCTTGTGGGGGAGTGGTGAGCACCCTGTTAAGGTGGTGGGATGGGGTGGAGAGGAGACAGGGTTCCAGCAAAAGCAAACTTCAGTAGCTGAGGATCTACTGACAGCCGATCATCATGATGGCTTCTGGGGGGAGGAAGTGCCCGTTTTCTTTAAGGGTACAGTCCCTAGGAGGTTGGCCACACTCCAGTAGATGTCCCACACCCAGGAATACACAGGCTGCACAAGTTGGACTCAGTGGGGGGGGGGCAGAGCTGGAAGGGGTTAGGGAGAGAAGTTGAGGTGCATATGATCAAAATACATTTTAAGTATGTATGAAATTCTCATGAATAAGAAAGATTATAATAAAAATTCAAAGCCGAGAACTATGTCAGCCTGGACCAGATAGGATTCTTGTCACCATTTATCAAGGGCTTCAATAACCAGAGTTCACACCTAACCTGCTCTCCCTCTGGTCCATGTGTCCTACAG
Seq C2 exon
GCATTGTGTTCCACTACAGAGCTATTTCCACACGCTACACACTGGACTTTGACCGAGCCCAGCGGGCTTGCCTTCAGAACAGCGCCATCATCGCCACCCCTGAGCAACTGCAGGCCGCCTATGAGGATGGCTTCCACCAGTGTGATGCAGGCTGGCTGGCTGATCAGACAGTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000028992:ENSRNOT00000047848:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.031 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0768612=V-set=WD(100=94.6),PF0019312=Xlink=PU(0.1=0.0)
A:
NA
C2:
PF0019312=Xlink=PU(60.4=98.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTACTTCATCGACCCCATGC
R:
CCAGTGTGTAGCGTGTGGAAA
Band lengths:
348-1730
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]