RnoINT0038910 @ rn6
Intron Retention
Gene
ENSRNOG00000058470 | Col12a1
Description
collagen type XII alpha 1 chain [Source:RGD Symbol;Acc:2374]
Coordinates
chr8:87114533-87115558:-
Coord C1 exon
chr8:87115394-87115558
Coord A exon
chr8:87114680-87115393
Coord C2 exon
chr8:87114533-87114679
Length
714 bp
Sequences
Splice sites
5' ss Seq
TCGGTAAGC
5' ss Score
9.86
3' ss Seq
TACTTAACTCTTTTGTCAAGGTA
3' ss Score
4.21
Exon sequences
Seq C1 exon
GCATGGCTTTGAATTTCATTCGCCAACAGAGCTTCAAGACTCAAGCTGGCATGCGGCCTCGTGCTCGCAAAATTGGAGTTCTCATTACCGATGGAAAATCACAGGATGATGTGGAGGCTCCATCCAAGAAGCTCAAGGATGAAGGTGTAGAGCTGTTTGCTATCG
Seq A exon
GTAAGCAATGGAGAAGGTAGTGAAGCCCTGAGGTGACAGCAACACCGAGGACATTTTCTGTATTTAAAAATTATTGGATTACCATGCTTACTCACACAAGGAATGGCAGAATTCTTGACCCTCCCAAACAGAAGTGTAGTGGAGAGGAACTGAAATTAATTAACAAAGGCGGGGGGGACTAATACTAATTCCAGCTCTCGTTCTTTTGGAATGGACAAGACTTATCTGATACCTGAGAAGAATCAGAGCTTAGAGAAAACAGAAGCTAAAGAAAAAAAAGACATACTTTGTCTTGATGGCAATAAAGTTATACAGTGGGATTTATTTGCCTACGAAAAGAAATTCTGGAATGAGAGAAAGGTGCTACATATACCTAGAGAAAACACAGCTCTGTCATGCTTTTTTGAGTTCATTATACAATAAAGGGATTTTTATATTTAAAAATACTACTGGGAAGGGAGAGATGGCTCAGCAGTTAAGGCTAGTACTGCTCTGGCAGAATACCTGAGTCCCATTCCCAGCACCTACATCGGGTGGCTCACAACCACCAGGGTATCCAAAGGGCTCTATGCATACCTGTACTCATGTGATTCTACCCAACAGAGGCACAGTGATGGAGCACTTGTAAAGAGAAAAGGCCTGGAGCATTTGCTTCATTCCATTGCTTTTTTTCCTGAAAGGTGCTTTCAATTTGTACTTAACTCTTTTGTCAAG
Seq C2 exon
GTATTAAGAATGCTGACGAAGTTGAGTTAAAGATGATTGCCACTGATCCAGATGACATTCACGCATACAATGTGGCAGATTTTGAGTCATTGTCCAAGATTGTGGATGACCTCACCATCAACTTGTGTAACAGTGTCAAGGGCCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000058470:ENSRNOT00000077071:20
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.089 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0009223=VWA=FE(31.8=100)
A:
NA
C2:
PF0009223=VWA=PD(21.4=74.0)
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:
GCATGGCTTTGAATTTCATTCGC
R:
CAGGGCCCTTGACACTGTTAC
Band lengths:
312-1026
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]