RnoINT0038906 @ rn6
Intron Retention
Gene
ENSRNOG00000058470 | Col12a1
Description
collagen type XII alpha 1 chain [Source:RGD Symbol;Acc:2374]
Coordinates
chr8:87115859-87117842:-
Coord C1 exon
chr8:87117721-87117842
Coord A exon
chr8:87116009-87117720
Coord C2 exon
chr8:87115859-87116008
Length
1712 bp
Sequences
Splice sites
5' ss Seq
CCGGTAAGA
5' ss Score
10.1
3' ss Seq
TCTTACCGTTGCCGTGCCAGGGA
3' ss Score
7.09
Exon sequences
Seq C1 exon
GGCAGGCACTACATATAGAGTCAATGTTTTTGGGATGTTCGATGGAGGAGAAAGTTTACCACTTGTTGGGCAGGAAATGACAACCCTTTCTGACACAACTGTGACACCATTTCTATCTTCCG
Seq A exon
GTAAGAAACCGAGTTGCATTTCCATGGGGAAATAGTAGTATGATGCTATTGCACATGTGAGGTGTGAGGCTATTAAACGATGACAACTGTGACTTTCACTACGATTTATTTAAATAATTGACAAACTTTTTTATGTTTGTAGAAACTGCTTCGAATGTCCAGTTGAGCCCAGTTTTTGGCTTTTCATTTTCAATTTTGCATTAATTGAATACTTGATTATTTAAAAATCAGTCCTTATTGGTTATTTTATTTAAAAAATTTATTTTATTAAGTGTAATTTTCTATTTTTTCTTTTTAGTGGTATGATTTTCTTTTGTTAAAATAATTATATATTTTTTACTTTGATGGCTTCCTTGGACTGAGAAAGAAGGCTTTATACATAAGGAACTGGGCACTCATGACTTAGAAGCCAACAGTAGCACAGTCCTTTAGATGGCTTGTCTTTGCCGTAATCACAGCTTCGATGTAGGCAAGCCAGCATTTAAGGCAATTAAAGGTGAGAGTAGGAGGTAGACTTTACTTCTAAACTTTAAAAATAATCACTTATTAAAACCAGTAGCTCTTAGCATAACGAGAGAAGTCAAGGCCATAAAGATGTAGGTTCCAGAACAATGTATGACAGTCTTCCATCATGAGAAGAGTCATACACAAATGGCACTAAAGTAATTGGTAGTGTGATGAGCATTTCTTGATTCTCGTTCATTTGAAAAGTGATGTAACTATGACCTGAAAACATTGCAATAAATGGGAAAGTTTCTAGCTGGGAGGCAAGCTTCAATAAAAAGAGCATTTACAGTTAAGGTGGATAAAGGAAAGTGTCAAATTTTGATATTTTGCATTGTTTTATTGTTTCTCTTATGATGATATTAACTGGCTTATATTTTTATTTTGTAGCTTCTCACTGAGGATATTGGGATTATTTTCTCTTCCCAAAGCACCTTAGCTTTGTATCTGTGTTTTTGTTCGTTGTCTCGACAGCTCTCAATTTGTGTGTTTCTCTGCATCCTTTTCCAAATGGTCTTCCTTCTTCTTCAATTCTTTCAATGTGCAAACTTTGCTGTCTGAATTTACCTAATTTTTATATACAGTAGGTGAAAAAGTTGATAGTTAACAACGAAATAATATAACAGTGTTTCAAGTTTTCAAAACATGTGTTTACTTCACAGAAGTCTGATTTTAACTATCATGTGCCCAAGCTTTCATAACACGTAATGGTAACCTGGTGGCTTAACTATTATAAAGGATATTTTTGGCTCACTGGAATCACTTATAGTTTAGCCATTTAACCAGTCCATCCTATGCTTGTTTGCTAATGTCTTAAATAGGGAAGGAGAATGGAACATCTTATAGCACATCCAAATCTTATTCAAATTATTAATATTTATTGTTAGAAAGGTATGCATTCCCATTCATTATTTTCAGTAATGATTGTTGGGTGAGCCTTTCAAACTGACCATCATGGTTTACCTAGAATCTCTAGGTTCTGTGATTGTGATCAGAAAATATAGTTACAGATGAAGAAAAGATTTGCAACTGAAATAATATTTGGAGAAACTGATTCTCATGAATGTTATTTAAGGTTCAGAAATTATAGTTGTGTCTTTAAATTATTAGACCTAGCTGCAGTGTTGAATAGACAACTTGGGTGGCACAGGGGTATGACCTGCCAACGATATGCTTCTTACTGTCCTATCTTACCGTTGCCGTGCCAG
Seq C2 exon
GGATGGAATGTCTCACCAGAGCTGAAGCAGACATTGTGTTGCTGGTGGATGGGTCATGGAGCATTGGCCGCGCAAATTTTAGAACTGTGCGAAGCTTCATCTCTCGTATCGTGGAAGTCTTTGAAATCGGCCCCAAGAGAGTACAAATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000058470:ENSRNOT00000077071:17
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.071 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0004116=fn3=PD(24.7=47.6)
A:
NA
C2:
PF0009223=VWA=PU(23.1=78.4)
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:
GGCAGGCACTACATATAGAGTCA
R:
ATTTGTACTCTCTTGGGGCCG
Band lengths:
270-1982
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]