RnoINT0039092 @ rn6
Intron Retention
Gene
ENSRNOG00000031475 | Col16a1
Description
collagen type XVI alpha 1 chain [Source:RGD Symbol;Acc:1310982]
Coordinates
chr5:148295423-148296937:+
Coord C1 exon
chr5:148295423-148295476
Coord A exon
chr5:148295477-148296892
Coord C2 exon
chr5:148296893-148296937
Length
1416 bp
Sequences
Splice sites
5' ss Seq
TCGGTAAGC
5' ss Score
9.86
3' ss Seq
CTGTTCCTTTGGGTCCCCAGGGC
3' ss Score
10.01
Exon sequences
Seq C1 exon
GGCATCAAGGGAGAAAGAGGATATGCTGGCCCTGCGGGAGAGAAGGGGGAGTCG
Seq A exon
GTAAGCTGCAGCTGCAGTGGGTGTGGGTGTAAGGAGAGCTTCAAACGGGGTGTCCCCACCCCGCCACCTTCATCAACTGGACTGGAGATCTTCCCACGAGGAGGAGCCCGCGACCCCTGCTGCCCCTGCCCGAGTCACTCCAGCTGGGGCTCTGCACAGGCTGGTGGCTGTGGCTGTGGAGGCGGAGGCTGTGAGGAGATCCCAGCAGGCTTCTTGCAGAGAAGGCGACTGAGGAGGGGAAGGGGGGGCCCAGTCAGCTGGCAGAATTCCCCTCTCCTGCCAGATCAGGGCCAGGGGCTTCTTTTTTCTATTGAGGCCACCTTCATGGGGGTCCTACGCTGAAGGAAGGAGCTGAGGACTGCTAGCATGTGAGGTCACAGGCTCCTGGGTGACATCATTCTCCCAGAGTCCTTTAACCAGCTGGGGAGTTAGTGGTGGGGGAGCCTGGGCTGGAGCCTGTGTCTCTCTGGTGAGGAACCTCACCCCTCATACCCGGGACCTGCCAAGCAGAACTGGAGCCTTAACTCTCCCTCTCACAAACGTCAGCAAGGCCCCATGGGACTCTGCCAACCCTGCCACCCTCTACTCTGCCACTGAATGGTCTCCTAGGCATGCTGGGTGCTGCGAGTCCCTGGTGGGGGGTGGACTGGGCAAAGGCCCTATGAGACTTGCCCTGTAGCATGAAGCAGATAAAACATGGGTGGATGGATGGATGGGGGAGGGGAGAGAGCGCGAGAGAGAGCGAGAGCGAGAGAGAGAGAGAAGAACGATGAGAGTGGAGAGTCCTGAGCAGAGTGGGGGTGGGGACTGGGGGGCTGGGGTGGTCTGAGGATGCTGTAGAAGAGGGAGAGGGGGTCCCCAAGGAGGAACAGGGGAGAAAGGAGCTGTGCTGTGCCCATAAAGAGCTGGAGGTGATGGGTGGGTCCTGGCAGGAGCAGCTTCGGTTCCCTAAGGGTTCCGGTGATGAACGGTGGGCATCGCAGGCAGGGGAATAGTAATGCACAAGCCTGAGGGTGTGACCCCATAGAGCATGTTCAGAGAACAGCAGTCTGCACAGAGCAAAGCCCAGCAGAGGAGGAGGCTGGGAGAAGGGTGGAAAGCAGGAAAGGGTGGTTGGTGACAGACTACAGGATGCCTGTAAATCCAGCATGAGTGGAAGGCGTACACCTCATTCATTAGACAGAGGGGAGCCATGGCAGGCAGGCTTTTGTGTCAGAGCCAGGCAGAAGAGAGAGAGATTAGCTGATATTTGTTGGCCAGATTGGCTAGGCCAGGAGGTAGCAGGATTAGTTAGCAGCTGGTTCCAGAGAACTGAAGGGCCTGGTGGAGAGGACACTCCCACCTCAGGCTCCGCCTACCCTGGGTCCTCATTCCTCATGTTTCTGAGTGATTGGTTCTGTTCCTTTGGGTCCCCAG
Seq C2 exon
GGCCCACCAGGATCTGAAGGCCTTCCAGGTCCCCAAGGTCCAGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000031475:ENSRNOT00000067663:52
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.791 A=NA C2=0.985
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(25.0=100),PF0139113=Collagen=FE(19.5=100)
A:
NA
C2:
PF0139113=Collagen=PD(16.0=80.0),PF0139113=Collagen=PU(21.2=93.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
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]