RnoINT0038905 @ rn6
Intron Retention
Gene
ENSRNOG00000058470 | Col12a1
Description
collagen type XII alpha 1 chain [Source:RGD Symbol;Acc:2374]
Coordinates
chr8:87117721-87118962:-
Coord C1 exon
chr8:87118770-87118962
Coord A exon
chr8:87117843-87118769
Coord C2 exon
chr8:87117721-87117842
Length
927 bp
Sequences
Splice sites
5' ss Seq
TAGGTAGGA
5' ss Score
7
3' ss Seq
ACTGCCTGTTACTGTTTCAGGGC
3' ss Score
11.38
Exon sequences
Seq C1 exon
CTTCTCGATTTAAATCGCCGAGAAACCTCAAAACTTCTGACCCAACAATGTCAAGTTTCCGAGTGACTTGGGAGCCTGCCCCTGGGGAAGTGAAAGGTTACAAAGTCACCTTTCACCCTACAGGTGACGACAGAAGACTTGGGGAGTTGGTCCTTGGACCATATGACAACACAGTTGTCTTGGAGGAGCTTAG
Seq A exon
GTAGGAATGAACTGTATTTGTGCTAAGGACTGCATCGTTTATGTGAACTAGTAGGTTTTACACAAAGAACTACCTCACGTTTGTAGAGACCAGCAAAGAATTAAGCTTGACAAACGGCTTGTATTGTTTAGATAATTAAGAATACTTGGATCTTGACATGTCTGTATCACATAGTTTCATTGCACTTGCAGTCATGTGAAAATCTGTGGCCAAGTGACTCATTCTGAGACGTCCCCCACCCCCATGGTGGATGTCCCAGCAGTGAAGCATACTGGAGCTCAAAGGCCAGAGTCTGTGCTTGCTGCCAGCTGGCAGAACAGCCTTGGGTTGATTAGAGGTCTAGTTTTAGACAGTGAGTTGGAAAACAAGGGAGTGTGAATTCGAACAGCACTCCACATTCATCCAGTGGCACCAGTGGGTTACTGTACATTCCTCTTGGGAATTTTGTTCACTTAAGTATTCATTCAGTAATGTTGGAACCTGTATAGTGCTTGTTGTTCCTGATCACTTGAGTAGGTAGGATGAAATTCAGGAGGTCACTGCTTGACATGGCCCAGTGCTGAGTGTCTCAGGTCATTGTGCAGACACAGAGCATTTCAATCACCCTAAAGCCCGCATCTCAGAAGCAGCCTAAGCAAGGCAGCTCATTCTTCCCAACACTGAAAGGTAACATGGGGGAAACGCTGCCTCTGAAAAGTCCTGGGACAGTGCAGTAAATCCCCAGAGCTCCCTGGAATGTTGGGTGGCTTGTTTCCTGTGACATCAGCAAGCTGGAATGTGATGGCAGCTATCTTTGTGCTTTTGCAATACTGAACATTTTACGTTCCTATGGGTGAAAGTTTGTTAGTGAAGATAAGTATCTTTAACAAGACGAGAACTGTCCTTTGAGACCACAGTCCACACCCACACTGCCTGTTACTGTTTCAG
Seq C2 exon
GGCAGGCACTACATATAGAGTCAATGTTTTTGGGATGTTCGATGGAGGAGAAAGTTTACCACTTGTTGGGCAGGAAATGACAACCCTTTCTGACACAACTGTGACACCATTTCTATCTTCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000058470:ENSRNOT00000077071:16
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.385 A=NA C2=0.071
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(74.1=92.3)
A:
NA
C2:
PF0004116=fn3=PD(24.7=47.6)
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:
ATCGCCGAGAAACCTCAAAACT
R:
CGGAAGATAGAAATGGTGTCACAGT
Band lengths:
302-1229
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]