RnoINT0011748 @ rn6
Intron Retention
Gene
ENSRNOG00000028992 | Acan
Description
aggrecan [Source:RGD Symbol;Acc:68358]
Coordinates
chr1:140821340-140822090:+
Coord C1 exon
chr1:140821340-140821498
Coord A exon
chr1:140821499-140822007
Coord C2 exon
chr1:140822008-140822090
Length
509 bp
Sequences
Splice sites
5' ss Seq
ACAGTGAGT
5' ss Score
8.34
3' ss Seq
AGCCTATCTTCCCATTCCAGAAA
3' ss Score
7.99
Exon sequences
Seq C1 exon
ACCAGGAGCAATGTGAGGAGGGGTGGACCAAGTTCCAGGGCCACTGTTATCGCCACTTTCCCGACCGCGAGACCTGGGTGGATGCAGAGAGACGGTGTCGGGAGCAGCAGTCACATCTGAGCAGCATCGTCACCCCTGAGGAACAGGAGTTCGTCAACA
Seq A exon
GTGAGTGTGACAGGGGCTAAGGGACACAGCAGTGAGAGCAGAGAGCCTGGCTGTTCTGAAATGAGCAGACTGGAGATCGGGATGATAGCGCACCTTGCATGTACCAGGTCCAGCATTGCAGGAAGGGGGAAGGGAGACGAAGCCAGAGAAAGAGAGTGCAGATTGGGGGCACTGCATGGCACGGAGCTGGAAGGTCAAATGCCCCCACAGTTTCCTCTGAGAAGAAGCCACAGATCCCTGGGACCAGCAGCCCCAGCTGACCGAGGGCAGACCCTGACAGTCAGTGCCATACCAGGTTAACCCTGTAGCTATCACCTGCCTATACCAGCCTGAAGAGGTGTTCCAATATATACCACAAACATGCATGTCCTGAGACCCTTGCAAGGTCCTTAGAAGCCAGTGGCATGCTGCTAGGAGGCACTTACCTCCTTCCTCCCTCTCCATGAGCTCCAGTCCCCAGACAGTGTGGGGTATCCAACATCAAGTGCAAGCCTATCTTCCCATTCCAG
Seq C2 exon
AAAATGCTCAAGACTACCAGTGGATCGGTCTGAATGACAGAACCATCGAAGGGGACTTCCGCTGGTCTGATGGACACTCCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000028992:ENSRNOT00000047848:16
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.250 A=NA C2=0.036
Domain overlap (PFAM):
C1:
PF0005916=Lectin_C=PU(30.2=59.3)
A:
NA
C2:
PF0005916=Lectin_C=FE(25.5=100)
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:
ACCAGGAGCAATGTGAGGAGG
R:
AGGGAGTGTCCATCAGACCAG
Band lengths:
241-750
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]