RnoINT0011754 @ rn6
Intron Retention
Gene
ENSRNOG00000028992 | Acan
Description
aggrecan [Source:RGD Symbol;Acc:68358]
Coordinates
chr1:140796193-140798301:+
Coord C1 exon
chr1:140796193-140796367
Coord A exon
chr1:140796368-140798173
Coord C2 exon
chr1:140798174-140798301
Length
1806 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
CCATATTGACTTCCCAACAGATA
3' ss Score
7.24
Exon sequences
Seq C1 exon
GCATTGTGTTCCACTACAGAGCTATTTCCACACGCTACACACTGGACTTTGACCGAGCCCAGCGGGCTTGCCTTCAGAACAGCGCCATCATCGCCACCCCTGAGCAACTGCAGGCCGCCTATGAGGATGGCTTCCACCAGTGTGATGCAGGCTGGCTGGCTGATCAGACAGTCAG
Seq A exon
GTAAGACCCTGACCCCCTGAAGAAAAACTGTCAGAGCTGACAGCCAGGTACCAGAGTCCTAGCAGAATGAAGCAGATGATGGGGTGGGACAATGATCTGCCCTGAGCTGGAATGAACATGATCCTCTGGCCAGTCTAGGGTCCAGCCTTGTCGACATACATACCCAGCGTCCCATCCCAGGTCCCCATTATTCACTCTCCAAGGCAAAGACAATACCAGTGGCCATGTTCTCAACTCCACCACTCTCTTTGCCTGTATTTCCTCTTGATGTTTCTTTGCTTCTGGTTTGACAGTGAGTTTTTTACTAGGAGTTTAATTTACTTTTGCTTATTGCCTTTTTGTTTTATTGCTTATTGCCTTTTTGTTTTATTTATATATAAATTATATATTATAACACATATTATAATAATATATTACATGTTTCATAATTTATACAAATATATTGCATTTATATTGCCTGCTTATTCATATCCTTTTTTGTGAGACAAGACATACATACACCAAGTGTCTAGAAACATCTTTTCTGAGGGAGTCCTAGGAGCCACACGGCAAAGCAGAGCAGACAGAAGCCTGCCTCAAGCATCCCAGTACAGTGCAGCAAGCCTGTGGAGACACTGTCCACCTCATGTGCATCCTAAGGGTAGCCCCAAAGCCGGCCCACAAGACCTCAGGAAGACAGCTGTACAAGCTGGGACAAGCTAGGGGATCTTAGGTCACAGCACTGTTACAGTTTCGTCTCTGCTGTTGAGATTAAACACTGATCAAACACAAGTTGCGGAGGAAATGGTTTTTTCCAGCTCTTCTTCCAGGTCGAGGTCTATCACTGAGTTAAGTGAGGGCAGAAACACTTGGAGGCAGGAACCATGGAAGAATGCTGCTTGCGGCTCACGGTCTGGCTCACCCACAGGCTCATTCTCAATTAGATTTCTCACACAGCCCAGGCCCATCTGTCTAGGGATGGTGTCATCCATTGTAGGCTGAGCTCTCCTATGTTGATCAGAGCTCAAGACCTCACAGACCTGGTCACAAGCTAATGTGAGCAGTCCCTCAATTGAGACCCCTTCGGATGACTCTAGACTATGTTGAGTTAACAGCTGGAGCTAACTGGGACAGGCACTTTCTATAAAAATTAGTAGATAGACCAAAAAAAAAAAATAAGTAAGACAACAGTCAAATATGGCAAGAGTCCACATATTGACCTCAAGAAGAGCTAGACTCTAATCCCAACCCTGGAATTTGGAAGCTGTGCATTTGTCAACAAAAAGGTTAGCATTTCTGGACCTTACTTCAAGTGTAAATAGAGACCAGCCCTTGCATCACTTAGTGGGCATAAGATTCATGTGGTACCAAGTAGGCACCATGGCCAAACCCAACCCAACCCAACCCATTCCTCCTTTCTGTAAATATCATCGTGCTGAAACCTAGCCATGCTCACTCGGTTACATGTTGTCTGCAGCTGCTCTGTGCTGCTGCAGTTCAAATGACACCACAGGGGCCCATGGTTTGCAAAACCCACAAGATTCTGGCCTTTTATATGGAAAGCATCTTCAGGGAGAGAGTGTTTGGTACCAAGAGCGCTTGGTAGGAGAGGCAGCCAGACTTGTGGGCAGCACTGAGACTGGAGGGATGGGACTGGAGGGATGGGACTGGAGGGATGGGACTGGAGGGACGGTTGGCATACACAGCAGACTTGGACAGAAGTAGTTTTATGCCTGTCTCCTCCTATGGAGGCAAAGGCTACAAGAACAGTGACTTTGGGCTTCCCTCTGTTCCTAGTGTCACACTCCCATATTGACTTCCCAACAG
Seq C2 exon
ATACCCCATCCACACTCCCCGGGAAGGTTGCTATGGTGACAAGGACGAGTTCCCTGGAGTGAGGACCTATGGAATCCGAGACACCAACGAGACCTATGATGTGTACTGCTTCGCTGAAGAGATGGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000028992:ENSRNOT00000047848:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0019312=Xlink=PU(60.4=98.3)
A:
NA
C2:
PF0019312=Xlink=PD(38.5=84.1),PF0019312=Xlink=PU(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCATTGTGTTCCACTACAGAGCT
R:
CCTCCATCTCTTCAGCGAAG
Band lengths:
303-2109
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]