RnoINT0040504 @ rn6
Intron Retention
Gene
ENSRNOG00000009531 | Col9a3
Description
collagen type IX alpha 3 chain [Source:RGD Symbol;Acc:1310255]
Coordinates
chr3:176114737-176116614:+
Coord C1 exon
chr3:176114737-176114808
Coord A exon
chr3:176114809-176116578
Coord C2 exon
chr3:176116579-176116614
Length
1770 bp
Sequences
Splice sites
5' ss Seq
CGGGTAAGG
5' ss Score
10.17
3' ss Seq
AGAACCTCCTCTCTGCCTAGGGT
3' ss Score
7.86
Exon sequences
Seq C1 exon
GGCCAAAAAGGCAGCATAGGAGACCCTGGCCTTCCAGGCCCCCAAGGCCTACGGGGAGATGTGGGTGACCGG
Seq A exon
GTAAGGGTCCTTGTGCCTCCCTGCTCTAACCAGTCTATATGACCCAAGCTAGCAGAAGCCCACGACTTCCCACATGGGTGGCAGGAGTGGGAGCACCCTGTTCACTGTCCACTTAGCCTCCCCACCTCCCATGGAGGCACAGCTGGGCTTCCTGGGTTACTAAGACTCCTAGAGCCTCCAGGAACTCCCTGAAGGACAGGGAACTCTGTGGACAGGTGCCCTTGACTCTTTTCTTCTTCATTCTCTTGGTCTTCTTCTTGGGCAAGAAGGGATCTAGGATTTTTTTTTTAATGTTTTATTTATTTATTATATATAAGTACACTGTAGCTGTCTTTCAGACACACCAGAAGAGGGCATCGGATCTCATTACAGATGGTTGTGAGCCACCATGTGGTTGCTGGGATTTGAACTCAGGACCTCGGGAAGAGCAGTCAGTGCTCTTAACCGCTGAGCAATCTCTCCAGCCCGGGATCTAGGATTCTTACTACCCTATCACAAGCCCTGCATGCAGGCCTGGAAGAACCAGTCACTGGGGCAAGGGAAGAAGTGGACACTTGAGGCTCTAGGTCCTAGGCTGCTGTTGGATGTGAGCTCAGACCTGAATGACCCCAGTGTTTCAAACATGTAACTTTCCAAGACCCTTTGCTGATGGTCCTACAGCAGCCAGTGGCATTGGCGTTCTTCAGGGACAGGGCCCAGGGGAGTTGTGGCTTACTCAGGTCCTCACTGGTTAGTAGATAAGGCCTAGGGTCCCCTGGGAGGAGTCTGGGGGTCTGGTCTGGGGCCTGGACCATATATCAGCTCTTTAGAGGCTATGTGATTGCTTTCTTGATTCCCACTTGGCAAGGACAGAGCACTCTTCAAAGGCGTGGATGCAACCATTGGAGGCTCTAGGGCACCTCTACAGACACAGGGAACCACAGAAACCAGTGCCACACAGCAGGGACAGTGGGTGCTTTATTAGTCTCTAGTCAGGAAATTCCAGGGGTTAGGGAATTTGCCAATAGCTCTGAGGGCTCTAAGCTAGTGGAGGGAAAAGATTGGTAGTAACAGTGATGTCTGTCCAAGCCCCAGCAGAGAGGAGACACTTTACTGGCTTTTTCTTCGTTGGGTAGCTCTTGCCTTTGCTTCCACACTTAATTCTCTTTTAAAAAGAGATTTATTTATTTTAATCTCATGTACATGATGCTTGCCTGCATGGATGTATGTGTACCATACACATATAAGAGCCCAAGGATGTCAGTCAGATGCGAGCCGTCTGATGCAATGCTGGGAACCAAGCCTGGGTTCTCTACAAGAGCAGCGAGTAGCGCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCCCTTGTGTGTGTGTGTGTGTGTGTGTTTGTGTGTGTGTGGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGATACACAAATCGCAGACTGCAGTAGCTGATTTAAAGAATTCACTGTCCACTGAGTGATAGGCAGCTGCTGTCCGGGGAAAGCTGACCCTTGAAGGACCGGTGGGGCATGGATGGCTGTATAATGCTGTTATCTATGGACTTGGGTTTGGCAACTGGGGCTGGGGTGCTGTTCCTAAGCCCCGTGTTACAGGAGGAATTTCTATACCTACTGTAGGTGGGACTCCTGCCTCTGCCGTGTAGGGCCGTGACCTCCCCCCACACAAGGGGATTCCCAGGGTTCCTCTAATCTAGAACCTCCTCTCTGCCTAG
Seq C2 exon
GGTCCAGGAGGTGCCACAGGTCCTAAGGGAGACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000009531:ENSRNOT00000013105:24
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(7.8=33.3),PF0139113=Collagen=FE(30.3=100),PF0139113=Collagen=FE(31.5=100)
A:
NA
C2:
PF0139113=Collagen=FE(14.5=100),PF0139113=Collagen=FE(15.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
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]