RnoINT0011751 @ rn6
Intron Retention
Gene
ENSRNOG00000028992 | Acan
Description
aggrecan [Source:RGD Symbol;Acc:68358]
Coordinates
chr1:140823646-140824441:+
Coord C1 exon
chr1:140823646-140823828
Coord A exon
chr1:140823829-140824302
Coord C2 exon
chr1:140824303-140824441
Length
474 bp
Sequences
Splice sites
5' ss Seq
ACCGTGAGT
5' ss Score
9.4
3' ss Seq
CCACCTCCCTTTTGCTGCAGCCA
3' ss Score
8.75
Exon sequences
Seq C1 exon
TGGCCTGTGGAGAACCCCCAGCGGTGGAGCATGCCAGAACCCTTGGGCAGAAGAAAGATCGCTATGAGATCAGCTCCCTGGTGCGGTACCAGTGTACTGAGGGCTTTGTCCAGCGCCATGTGCCCACCATCCGGTGTCAGCCCAGTGGGCACTGGGAAGAGCCTCGAATCACTTGCACAGACC
Seq A exon
GTGAGTATTGTCCCCCTGGTCCCTCAAATGGTACAGAGTCAGGCTCCACCAAAAGGGCCTTCTTGCTCTCCCCAGAGCATAGTGGTAGCTGGCACTGTTCTGTAGCTACCATACCATGCTAGGGGCTAAGCCACACAGGGATGGCTTAAGGGTCTCTCCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAACCACCATTGGTCCCTACCACAGGGAATGCTGCTGTTCTCTAAAAGGAGATAAGAAAGCTGGTAGCCTGGGCTCTGACTGTCTCCTGAGCCTAAGGAAGTTTAATGAGAAATCCAGTCCAGAGGAGCAGGTTGGGAGCAGCTTTGGGTTACGTTCTGAGACCCACGATGCACAAGGAGGGGCTCCTGCACACATGGGAAGGCTGCGGGAGCCTAAGCTTGGCCCTGCTTCCTCCCCTCTCACCGTTGCTTCCCACCTCCCTTTTGCTGCAG
Seq C2 exon
CCAACACCTACAAGCACAGGCTACAGAAGCGGAGCATGAGACCCACACGGAGGAGCCGCCCCAGCATGGCCCACTGAGAGGAGCTTCCACAATGTGCCCAGGATGCTGAGCCCAGCGGCCAGCCATGCTGACCGTGCAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000028992:ENSRNOT00000047848:19
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.177 A=NA C2=0.800
Domain overlap (PFAM):
C1:
PF0008415=Sushi=WD(100=91.9)
A:
NA
C2:
NO
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:
GCCTGTGGAGAACCCCCA
R:
TGCACGGTCAGCATGGCT
Band lengths:
319-793
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]