RnoINT0038912 @ rn6
Intron Retention
Gene
ENSRNOG00000058470 | Col12a1
Description
collagen type XII alpha 1 chain [Source:RGD Symbol;Acc:2374]
Coordinates
chr8:87111437-87112204:-
Coord C1 exon
chr8:87112065-87112204
Coord A exon
chr8:87111567-87112064
Coord C2 exon
chr8:87111437-87111566
Length
498 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGC
5' ss Score
8.7
3' ss Seq
CTTTTTATTTTCCCTTCTAGTTT
3' ss Score
11.12
Exon sequences
Seq C1 exon
GTGACTTGGAAGCACCATCTAACTTAGTTATTTCAGAGAGAACTCATCGTTCTTTTAGAGTGAGCTGGACACCCCCTTCTGACAGTGTGGACAGATACAAGGTGGAATACTATCCTGTCTCTGGAGGGAAACGCCAGGAG
Seq A exon
GTGAGCAGGTGACCCTTAAGCACTTCTTCCCTACGGTGAGACTGAGTGATCCTCATTCGAGCCCAGAGCAAAACGTTGGGTGAAAGACAAGAGAGGAATGAAGAATGGTACTCTCTGTTCCTCTCAAGGCAGGCACTTCTGTTCGGACCTCATTAAAGGGAACTAGCTTTTAAAAATGTTCTTAATGGTTTCTACCTACTGTAGAATATCAGTTCAAGTTTTCAAACAAGTTAATTGATTTGTAAGTTTGGACTAGACTTATAAAGTTGACAAGGGAAACTTATTAAAGGTGGCAAATTTAACTACTTTTCCAGACATGGATATCACAGCTGCGAAAATAAATTATGTTGTCACCTGAGATCTTTCTGTAATCTAGTAATTTCTCAAAATAAAGGTCAAGGCCTCATGGGATACCTTCTAAACTTCCTGCAGGTGGCTGTTTAGGGATCGGCCAGGAGGAATGGAGCTGAGTGTTATTCTTTTTATTTTCCCTTCTAG
Seq C2 exon
TTTTACGTGAGTCGACTAGAAACTAGCACAGTGTTGAAGGATCTGAAGCCCGAGACTGAGTATGTGGTGAACGTGTATTCTGTGGTTGAAGATGAGTACAGTGAGCCTCTGAAGGGCACAGAGAAAACCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000058470:ENSRNOT00000077071:22
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.106 A=NA C2=0.091
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(53.8=91.5)
A:
NA
C2:
PF0004116=fn3=PD(43.8=79.5)
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:
TGGAAGCACCATCTAACTTAGTT
R:
AGGTTTTCTCTGTGCCCTTCA
Band lengths:
264-762
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]