RnoINT0038911 @ rn6
Intron Retention
Gene
ENSRNOG00000058470 | Col12a1
Description
collagen type XII alpha 1 chain [Source:RGD Symbol;Acc:2374]
Coordinates
chr8:87112065-87114679:-
Coord C1 exon
chr8:87114533-87114679
Coord A exon
chr8:87112205-87114532
Coord C2 exon
chr8:87112065-87112204
Length
2328 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGC
5' ss Score
8.69
3' ss Seq
CCTCTTATCTTCACACACAGGTG
3' ss Score
9.1
Exon sequences
Seq C1 exon
GTATTAAGAATGCTGACGAAGTTGAGTTAAAGATGATTGCCACTGATCCAGATGACATTCACGCATACAATGTGGCAGATTTTGAGTCATTGTCCAAGATTGTGGATGACCTCACCATCAACTTGTGTAACAGTGTCAAGGGCCCTG
Seq A exon
GTAAGCTGGGACAGATACTGGCATATCTGGGTAGGGACCTCTTCATGAAGTGCTCAGTGGCATCAGAGGCTCCCCTGAGGTGGAGTCCCCTGAGGAGTCCCCTGTGGTGACTAAATATAACACTGTAATTTATAGTATTTGCATCGGGTACATGGTAACTAGTTGAAGGCTTTGTGAAAATTATGAAATTTGGTTCTTGTTACATGTGCAAATTCCTTTCTTTTTATACAAGAATATTATAGTAAAACTGCCCTCCATTAATTTATCTTGGATCTGGGAAAGTCAGAATAAATTTAACCTCATAGAAATAGTAGAAATGGTTCCAGATATTTGCAGAATTGTCATTACTGGCACTGGATGTCTGCTTTGAGGAACTTTCTAGTTAAGGGTCAGTGCTTTAGTTCATTTTAAAATGATTTTTTGGAGGGAGGCAGGGGCGGCACCAAACTAGGAAATGACATCTAGCTTATTTAAGGATTTATTTACATTATATGGCAAGGTCAATGCAAACAAATGTGGGAAGTGACTAAAAAAAGAAAAAGAGAGGAAAGAGTTGACAGACGCAGTTTCACTTCAGTCCTACTTTACTCAGATGCTGCGACTTGCAAGTTGATGAGTTTGGCTTGCTCAGTAATGCTTGGTAGCTTCCTAATGTATAGGACTGGGAAAGACATCTTACGTCTGCTTTCCTCTCTTCAGCTGCAGATTGTCAGATTTGATGCTCTGCACTGATAACCCCTGAATGTAAAGAGAAGTTACAGCCTTAAAGCTTAGACCATATGAAATCACAAGAAGACGTAGAGCCAGCGAAGTTGCCTAGTTAGGGTCAGATGGTTAGAGGTGCCGTTGTGGGGCTTTGAATGATGCAACCACGGAAAGGGATTGCAGTTTAGAAACCATTTCAGAACTGGGTTTGTAGTGACAGCAGAGGGTCAATATCTGCGTAAACCATAGGACAAGATAATGGAAGCGCCAACACTGAAGAGTTTTGCAAAGTTAACGGTAAGTCCATGATCCTTCAATGGCGAGGACATTTCTCTTAGGCGTGTGGACTGTGTAGAAGCAGTCTGTCATTAGCTTACAGTGGTTTCAGGGATGCGAGGTGGCAAAGTGCTTCTCAAGGTCTGTGTCCTTGCTTACATCCACTTGTATGTTTCATGTTCCTTCTTGTACGTCTGTCCTCAAACTTTTGCAGATATTCTTTTTTGAATTTTGAACAGCAGACTGACCTTTCCCCTGCAGAAACAGACAAGCTGGGCAGTCAGAATTTGTAGACTTCTGGCTTTGGGTGAACTAAGAGAATTGTCTTTTTTTTTTTTTTACTCAGTTGGAGTGAACTTTGAGTGGGGATGAAAACATCTTTTATCTATTTTTTCCTTATTTTTTGTCAACTATGTAATAGTTGTAATCATTGAAGTTTCCTTGGCCATAAAACAACTTGATAATTTTGCAAGCTTGACTTTGACACAAGTGCCAAGAGCAGACATACTCACTCAATTTGGGCTTACAAAGAAACCCAAAGGAGTTTGTATGAAAGTGATTTGTCATGCTCGTGGAGTCATAGAAACAACTCTTTTCTCTTTAAATCATTATTTGTAACATCTTGCTGTTGGACTTAATGTATTTATCACATCAATTTTTTATTTTCTAGTTATTGTTACACATTAATTATTTCACCCATATCTTCCTACAGAAAGCACAACCACAGGGCTATTTAAGAATATGTATCACCACATTTAAAAATATTAATATTTGCTTGTTTTCATCCTTCTTAAACACATAAGAAGTAAGTGCTCTAAAGAAACTCAACAAAGACAAGGCATAGTGCTATCTTCATAGAAGACAACATGTGTAGACATGGTAATGGGGTAGGGAACATGGTCTAACCTCATGAGACCATGGAAAAGTAGAATGGTCTGGATTTAGGTATCTTCTACTAATTAGGTAGAAGGGGTTGAGAGAGGACAGGGTGTCAGAGATGACTCAGAGGTTTTGGGTCTAGGTGACATTTTTTTTCTTTTTTTTTTTTTTCCGGAGCTGGGGACCAAACCCAGTCTAGGTGACATTTTAACTAGTGGTTTCATAGAATAGGAGATCATGTTTAAAGAAGGACAAAGCACTCTAGCTTGACTCTTCTGAGACTAAAGGAATCCTTTGGCCATTTATTCAGAGATGCCAATGGGCAATGGACCTCTGTAGAGATTTGTCGTCCATTTCCCATGTCAAGGGAAAGATCCTGTGTAGATCTGCACTGTTTTAAGTTAACTACATCTTTCACCACTCTGCTACAGAAATGAAGGTGTGTGTACCTCTTATCTTCACACACAG
Seq C2 exon
GTGACTTGGAAGCACCATCTAACTTAGTTATTTCAGAGAGAACTCATCGTTCTTTTAGAGTGAGCTGGACACCCCCTTCTGACAGTGTGGACAGATACAAGGTGGAATACTATCCTGTCTCTGGAGGGAAACGCCAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000058470:ENSRNOT00000077071:21
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.106
Domain overlap (PFAM):
C1:
PF0009223=VWA=PD(21.4=74.0)
A:
NA
C2:
PF0004116=fn3=PU(53.8=91.5)
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:
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]