RnoINT0038918 @ rn6
Intron Retention
Gene
ENSRNOG00000058470 | Col12a1
Description
collagen type XII alpha 1 chain [Source:RGD Symbol;Acc:2374]
Coordinates
chr8:87096509-87097387:-
Coord C1 exon
chr8:87097248-87097387
Coord A exon
chr8:87096642-87097247
Coord C2 exon
chr8:87096509-87096641
Length
606 bp
Sequences
Splice sites
5' ss Seq
GAGGTAATG
5' ss Score
8.73
3' ss Seq
TTTTTTCCTCTTTGTCTAAGACC
3' ss Score
5.95
Exon sequences
Seq C1 exon
GGCCTGTTCCAGCCCCAACCAACCTACAGTTTACTGAAGTAACTCCGGAGAGTTTTAGGGGAACCTGGGATCACGGTGCTTCAGATGTGTCTCTCTACAGAATAACCTGGGCACCTGTCGGAAACCCAGATAAGCTGGAG
Seq A exon
GTAATGTTAGCTCTCTCCGTCTCTCCCTTCTGTCCCATTCTCTCTCCATTTGTTTAAAGGAAAGCCCAGCTGAAATACAGCTTATTTCTGTGTATCAGTGACTTTCTGTTGTGAGAAAGCACCATGGTCTAGGCAACTCAAGGAAGAGCTGATTTGGGCTTAGAGTTCCAGAGGGACAAGAGTACATTATGGTGAGGGGACCCAGGTAGCAGGCAGACGTGGCGGCCAGAGCAGGAAGTTGGGGAATCATGTCCTCAACTGCAAGCTAGGAGCAAATTAGAATTGGAGCAAGGTCGTAAGCTCTTAAAGCCCGCCTCCAGGGTTGTACTTCCTCTAGCAAGGCCACACCTCCCTTTGGCCTCTCCAAACAGCACCATCCACTGAGGACTGAGTATTCAAATGCCCGAGTCTACGGCAGCCATTTCTTTTTCAAAGCACTACATACCATTACAGATAAGTCATCTTTGACAAGTGGTTTTGGGCTCATGCTCCTCTAATGGTGCAGAGGAACAGTCCCCTGAAGATGTCAGCACAATGTCATGTGTATGCATGATCTGAATGGTATTAATTTAGTATGCATGTGATTTTTTTTCCTCTTTGTCTAAG
Seq C2 exon
ACCATCTTAAATGGAGATGAAAATACCTTGCTGTTTGAAAATCTGGACCCCAACACTCTGTATGATGTCTCCATCACTGCCATTTATCCCGATGAGTCTGAAAGCGAGGACCTGAGTGGCAGCGAGCGCACAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000058470:ENSRNOT00000077071:28
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.426 A=NA C2=0.667
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(53.8=91.5)
A:
NA
C2:
PF0004116=fn3=PD(43.8=77.8)
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:
CTGTTCCAGCCCCAACCAAC
R:
CTCGCTGCCACTCAGGTCC
Band lengths:
263-869
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]