RnoINT0011747 @ rn6
Intron Retention
Gene
ENSRNOG00000028992 | Acan
Description
aggrecan [Source:RGD Symbol;Acc:68358]
Coordinates
chr1:140818264-140821498:+
Coord C1 exon
chr1:140818264-140818377
Coord A exon
chr1:140818378-140821339
Coord C2 exon
chr1:140821340-140821498
Length
2962 bp
Sequences
Splice sites
5' ss Seq
TCGGTACGG
5' ss Score
8.77
3' ss Seq
GTCCCTGACCTGTGTTGCAGACC
3' ss Score
9.55
Exon sequences
Seq C1 exon
ACATTGATGAGTGCCTCTCAAGCCCTTGTCTGAATGGAGCCACCTGCGTGGATGCCTTGGACACTTTCACATGCTTATGCCTTCCGAGCTACAGAGGGGACCTGTGTGAGATCG
Seq A exon
GTACGGCCGTCTCGGCTTCAGCTAATGTCACTAACTGCTGCCCTTCTCTTTCCTCACCCCTTCCTCCTTCTAACCACAGGTTCCAGGCCTGGGCTGGGGCCCACAGGTCTGCCTGGAGAGACATTCTGGGGGACACAACTGAGAAGCTTGCCTCCTGATTTTAACTCTTGTTCTTGCTCTTTCCCCCTTGGGGACCTTCCCCTGAAATGTTGGCTGATCTGACAGAGGAGACATGTGTATTTTGTGAAGTGGGGCTCGGGGAGTCTTGCAACCACTAATCTTTCTCCAGGGCTTGCAGACTTGCTGGCGGGACCACAGAGCTCAGTGCATGCGTCCCGCTAGAACAACACAGCACCAGTCCTGGAGGAAATTGTGGGTAGGCTCAATGGGTTCTCACTCTACTGACGGCCACAGATCTTCTTAGCATGATCATGGCACTGTCTTGCTGAATTCTCCATGGGAGTTCCATGTCCTTTCCATGACCCTAGGGAGCCACAATACCACGCTAACCAAGCTGTCCTCCTCTTCTCCTGGCATGAGGCTGTGGTTGGTCAACTGTGACTTACATCACCAGTATGCTCCAATCATGCATGAACAGGGACGGTGCATGCCATCCTCTCTCCATCACACCACAGTGGCTGCCTTCCCAATGCTACACTGGTCCATGCTTTCTTTCTTGCTCCCTTGTACAAAGCAAAAGGCTAGCCTGGCAAAGTAGTTTTGTTGCAAGGTGCAGGGGCTGAGTTTCCTCTGATGGACCTTGTCAACACATCTGCTTCTGCATCTGTGGGCCAGGAGCCCTAGACAGTGACACCCAGCACTCTCACTGATGGTGCTTTCTAAGCTCTGCCAGCTTCCCTGGCCTCAGGCTTTCCCAGTGCAGAAAAGGAGACCTGAGGCATTAGGGTGCTGGTAGCAGTAGCTCCTAGAAAGTTGGAAGTGTTCATGGGCTCAAAACCCTGTTGAACAAACTCTTGTCAGAGAAATTTCCAGAAAGCAGCTGAAAGTCCTGGCAAATCTTCCTTTGAGCCTGAACAGTGTGAGGAGGTAATAAGAATTATACATTCCTTGGGGGCATTGTCAAGGGATGGAAGAACTTAGGGTTTCTGCAGTAATGCCGGGGCACTCATCTTCCCTGCACCTCCTATCTTTTATCTACACTCCAAGAAGTCAGGTGCATGGGGTCTCCGCTAGGCAGGAATCAAAAGTACAAAGATTTCCCCTCCAAGATGCTGTATGGAGAAAGGTCTGAAACATCCACACAGACAACAGCTCTGGAACTCATCTGGGAAAGGAAGCCTCTGCTGCAACAGGAGCTGGGTTCCACAGGGGCCAGACTCTGCTTCCTTATAGACCAGAAAATTGGTTCCAGAGCCACTCACCTGAGCCCTAGGCCTGAGTGCCCAGGGAGGGAAGGCTCTGTCACAACCTGAATGCAATGCCTCATGCGATCTTGTCTCAGGCATCACTGCTTTCTCCAGCCTCTTTGGAAGTCTGTCTTATGTTCACTTCCTCTACTGGCATGGTCCTCCCAACCATGCCCAACTCCTCCCTTCCCTGACCCTACCGACCCATCTCAGCCCTCAGGTTCTGAGGTGGCACAAACCCTGGCTCACAGGTCCGGGGATGGTGTCACTGTCTCAGTGCTGTGAGTCCTCTGAGGCCTCCTTAGCCTCTTTCCAGACGTTTATCTTGACCCTTGAGGAGGGTATCAGAGGGACCCTCCTCCTCCTGGGCTCCACTCTGACTCTTTCTTCTCCAGGAGCCAGCCTTCTACTCCCTTTCTTTCCCTTTCCAGCCTAGCCAAGCACCCATCTCTTAGCCCAAGGGAGACTCCTTCCCCTCAGGGAAACCCCGTCCTTCCTGGAACAGCCAGACTATTGAAACTACCGAATTTGGAAGCTGCCACTCATCCTGAAGTATCTGTGGCAGCTCCCCAGCCCCACAGATGAAGGCTCCAGGCAAAGACGGAAAAGAGATAGATTTAGAGCTCCCTCTGTCCGGTGCTGTACTGGCAGATGTTTAACTATTGGCTCTCACAGAGGAGAGGGAGTCCTAACAGGAGGCCTCTTTCCAGTGCGGAGGTAGCAATCCTCCCACCAGGGCCAACCTACAGTCATCCACATGCTGCCACCAAAGGCAGTTAGCTCACAAACTCCTCTTCTGATCCTGAAGCTGGCTCTAAGATGTCCCCTCCTCTGTCCCTGAAGATCTAATCCAGACTCCTCTGTCCAAGACTCTAATCCAGGCCCTCCTCCAGCACACAGCATCTTTTTCAAATGAGGCCATGGTGGCGCTCCATTAGAGCCAACTCAGAGACCTGGGGCAGAAGCAGTTGCCTAGCATGGCTGAGGCCCCAGATTTCATCCCAGCGCTGACAGAATAATTAGAATTAAACTAATAATATAACAACAGCAACCAGCTCAGACCCGTGACCTAAGCTTGGTCTTCTTTGGACTCCCAAGAGAATTATTCTTGAGAGTCTCTGGCCTCACACAAGATTCTGTGAGGAAGAGGGTACCAGCTCCACCATGCCCATCCTCTTCTCTGACTTCCACCTATTACTACCCACAGCTCCTTTTCCCAGAATCCATCAGAAACTCGGAACTATGTTTTGCCTTAAATTTCAAAACCTCCCATCAGACTGTCCCTTTGTCCCCCAGTCTGCTGCACTCAGCCAGCCCTCTGCTTACCCACGCAGGGCATGAATCCATCCACAGGAGGAAATCTTGGGAGGCAAGGTGCTATATCCGAGAAAGAAAAGACCCTTTCCCAGGTGGCATGCACAAGGAGGTCTCCATAAGGCTTCCTACTTGAGCCTCTCTCTAGCTGAGCCTGTTGTCTCCCTCCGGGGCACAGCATTTAAGGTGGATTAAACATAGAAGTCCATGCCACAAGACTGGCAGGGACCACACTCCCAACCGGCCTTACCCCCTGTTCAAGTCCCTGACCTGTGTTGCAG
Seq C2 exon
ACCAGGAGCAATGTGAGGAGGGGTGGACCAAGTTCCAGGGCCACTGTTATCGCCACTTTCCCGACCGCGAGACCTGGGTGGATGCAGAGAGACGGTGTCGGGAGCAGCAGTCACATCTGAGCAGCATCGTCACCCCTGAGGAACAGGAGTTCGTCAACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000028992:ENSRNOT00000047848:15
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=0.250
Domain overlap (PFAM):
C1:
PF0000822=EGF=WD(100=79.5)
A:
NA
C2:
PF0005916=Lectin_C=PU(30.2=59.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
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]