RnoINT0040514 @ rn6
Intron Retention
Gene
ENSRNOG00000009531 | Col9a3
Description
collagen type IX alpha 3 chain [Source:RGD Symbol;Acc:1310255]
Coordinates
chr3:176105315-176106405:+
Coord C1 exon
chr3:176105315-176105368
Coord A exon
chr3:176105369-176106369
Coord C2 exon
chr3:176106370-176106405
Length
1001 bp
Sequences
Splice sites
5' ss Seq
CGGGTAAGT
5' ss Score
10.75
3' ss Seq
ACCCTTGTTTTCCTTTTCAGGGA
3' ss Score
13.29
Exon sequences
Seq C1 exon
GGTCTGACAGGGAGAGATGGACCCGCAGGACCCAAAGGTGCCCCGGGAGAACGG
Seq A exon
GTAAGTGTCTCAGTTCCAGTGGCTGTGGTCCAGGGATTGGGTTCCCAGGTGGCTCACAAGGCTGTCAGGGTAGACGTTCTGTGGATGGTGTCCATGGTTGTACTTGCTGGGCCCTGTCCCATTGCTCCGTTTCAACGGGGCATGGGGGGATGCTGAGTGCACAGCCCCTGGGTCCTCCTCACCAGAAACCTCACAGCTACACCTGGTCAGTGTGATCTTAGCACTCAGAGCAGGCGGAGCTGTGTGGCACTGATGGGAGCACAGGTGTCCCTCCTCTCAGCACAGAAGGAGCCACTTTACATCCCTGAGTCCAGCCATCTTCACTAAATCCCCCATTCCCTAGCGAACTGGCTCTCTCTCCCCAGAGTTCCTGAGGGCAGGGCTGTGTCCACCATTCTCCTTCACCTCAGGAGCACCGAGAACCCCCAGAGACCCAGAGAGCAAGAGGGGTGGGCGGGGCACAAGGACAGAGCTAGCATGGGGACTAAGATGTGTGGAACACCTGAATGAAAACAGCAAGCTGGTGACCGGTTGGACTGCTACTTGGGACGGGCAGGTCCCAGGCTGTCTGGGGGATACTGTGACTACAGTATAAGGACCAGCGTGTACCCGCTTCTTGGTAAGCCAATCGTTTCAAACCTGTCTACCAAGCCGGTAGTTGTCTCACATAAACCGAGGCCTGGATTCTGAGGAACCTTTGCAGGCTGGTGTTGACATAGCTTCCGGGAAGGCAGGCTAGGGTCCCTAACTGTGTGACTCACGCTCACCTTTGTGTCTCGCCCCTCCTGTTGACTCTGCCCACCCACTAGCAACTTTCTTGGCCCATGCTTTTCCTCCACACTCACAGAGGTTTCTAGGACAACAGAACTTCACATGGCTTCTGTTCTCTCCCTGATCCCCCCACCTTGACAGAGTTATGACTTAGGCTCCAAAGGAAAGAAAATGCAAGCAAAGGCCGGAGTGTCTTCCCTGTGTACCCTGACCCTTGTTTTCCTTTTCAG
Seq C2 exon
GGAAGTCTAGGACCTCCAGGGCCACCAGGACTTGGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000009531:ENSRNOT00000013105:5
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=FE(25.8=100)
A:
NA
C2:
PF0139113=Collagen=FE(16.7=100),PF0139113=Collagen=PU(3.4=16.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
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]