RnoINT0039312 @ rn6
Intron Retention
Gene
ENSRNOG00000010326 | Col20a1
Description
collagen type XX alpha 1 chain [Source:RGD Symbol;Acc:1563901]
Coordinates
chr3:176494768-176497388:+
Coord C1 exon
chr3:176494768-176494855
Coord A exon
chr3:176494856-176497277
Coord C2 exon
chr3:176497278-176497388
Length
2422 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGG
5' ss Score
10.51
3' ss Seq
TTCCAATCCTGTTGTTACAGTAA
3' ss Score
4.39
Exon sequences
Seq C1 exon
CTGCTCAGTATGAGCCTCCAAGGCTCCTACCTCCGCTTCTGCCTCTGGATGTTCTTGGGCACCACCTTGGCACTGGGGCAGGGACAAG
Seq A exon
GTAAGGAGGCAACGCCCCCACTGCCTGCAGAGGAACTCTGCTGCAAGCCTTTGACTTGCCAGAAGAGGCATTGCCCTGTAGAGTAAATGCCAACTTAGCCGAGCTGTTGCAGCAACAGGCAAGCTGGTAAAACAGAGGAGAGAATCCCCACTCTCAGCTTTTGCCTTGACCTTTGATCTTGTGGTCTTTCAGCCTTGCTTAGGGAGGCTTTTCTGTCTGAGTTATTTCAAGATTACTGGCATACTCCACATCTGATCCAGAATCTATGTTTGCTTGGTTATTCTGTCAACTTTTCAGTGTGGTTTCAGACACTGCATGCATGGCTTAGTGGAGATCAACACTCCTGCTTCCTGCCTCCCAGGAAGAAAAAGCCTTCCTACACTGTCTTAGACGGGTGGTGCATCTCTCTTCTCCGTACATGTATTAGGACAAGCGTTTCCATCTAATCCCTTCCTATTTGGCCATTCCAGGCTCCCCCTGGGAAAGTCTCCCCTAGTATTTTCTATGACCCCCAAGGGATATGCACAGGACTTGCAGAGTCTGTGTTGCAGACTCCTTCTTGTGGAGCTGCTGGCTCAGGTGGGTCCCTGGAACGAATGTTTCTGTGTCCCCAGAGCCTTCACACTCATGGGTACATCTAGCTTCCAGGAGCAACATGTATGTTCCTCATGACACCTGACTGATTTGAATCTGTTTCTGGAATTACACCAAGGTCTAGCCTCATCCAAGTTAAAAACTTCTCCTACCACTGCTATCCACAGCACTGCCTGTGGTTCCAACTCAGGGTTGCCTGAAGCCTAACAGACCTCACTTCCCAGCAATTCCCCTTATCCAGGGAGGTGACTACCCCATGGCCAAGTCCCTCAGCTCCCTTTGTTCAGACGGAGGAACCCCAAGGTGGGGCCTGTAGGTTGAGGTTTCAATTAGGAGGAAGGCTTTGCTGTATGAACAACTTAGAGTGATTCTGTAAGGCCCACAAATACTGTTTCCCAAGCTCAGGTCTCAGCATGACAGGCTACCCATGCATGACTGGGGTGGGCTGGGGCCTCAGAGACCAGCTGGGAGGTGCAGCTGAGGTTAGGGAGGGGATCGTTACTGTACTGTTTCTGAGACGGAAGTTCTAAAATCCCCTAACACACTGAGGGAAGAAAACAGAAGGCTCTTTATGGGCAAGAGTGGGGATCCATGCTCACAGCTGGCCTGTCAGAACCCCCACCTCATCCTGACACATTCCTGCCTTTCAATAGGTCATGGTCAGAGCAGTCAAGCCCATCCAGAAAGAGTTCATTCTGAATGGGTTATTGTGTCTACCCCAGGCACCCCCTAGTCTTTGCCTATCTCTTTGTGCCCCAGCACATGGTGAGGAGACTAGAAGAGGTCTCTGTCCCCATTTTCCAAAAATATCTGTCTGCAGCACAGAGTCCGGAAGCTTCCTGGGAGGTCAGCACAGGCCCTACGGTCCTCCTCCTCCCCATTGACCATGGCTTCCCCCTCCTTCATGACAGGATTACCCTGTCTTTGCTTCTTTTCCTTTTGCTGTGGCAAAATGCTAACAAAAGCAACTTATGGGGTAAAGGTTTATTTTAGTTCATCATGGCAGGGAAGCCAAGGTGCAGCCAGTCACACTGCATCTACCATCAGAAAGCAAAAAAGGAGTGAATGCTAGTGCTCAACCCATTACCTCAGTTTCTTATAGCTCCTGCCAAGGGAATAGCCCCATCTGCAATTAAAACGTGTGTCTCCACATTGTTAATGTCAATTAACGAAATCAAGCTGCTTCCCTCTCTCTAATCCCCCCACAGGAATCCTTGGAGTCTGATATCCCAGGTGACTTTAATTCTCTAAAGCTGACGGTACTAGACATCACACTGCCATTCCTAGTTTGGGAGCTGAAGCTTGGTACACATCCCACACATGTCTACATGTAGGCACACCATGTGCACATAAGCAGACAGCCATCACCATAGTTCCAGCTGAGGTCCTACATCCAATCTGCTCACAAGGGATACATCCACCTAGCATATGCATGCGTGCGTGCGTGCATGTGCCTGCACACACACACACAGCTGCTTCTATATCCCTCGAGAGTGGGAGACCCAAGGCAGCTGCCAAGGCCCTGGGCTTTATCTCTGCATCTCCAGTCATCATAAGGCGTACACACACACACCGCCTTCCCCTGGGTGCTGGTGTGATCCTCCTTTGCAGTGGTGGAATTAGACCCCCTCCTCCTGAATCTACCAGTGTGGCCTTGTCATCAAAGATCACAAGGATGTGGGAGCTTCATGAGGCCACAAACTCTATAAAGACACCTAGGTGGGGCCGTATCCCTCCATGCCTCTTAGGGAAAACCTCCTTCTGGAGGTGGTCAGTTGGTCACTGGTAAGTCTGCTTCACACCCCAACTTCCAATCCTGTTGTTACAG
Seq C2 exon
TAAGTAGCCGTCTGAGGCTGGCAGTACTGCCCGAGGATCGACTGCAGATGAAGTGGAGGGAAGCAGAGGGAAGTGGCCTTGGCTATTTGGTGCAAGTGACACCTATGGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000010326:ENSRNOT00000040270:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(0.1=0.0)
A:
NA
C2:
PF0004116=fn3=PU(48.1=97.4)
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]