RnoINT0039223 @ rn6
Intron Retention
Gene
ENSRNOG00000012759 | Col19a1
Description
collagen type XIX alpha 1 chain [Source:RGD Symbol;Acc:1308920]
Coordinates
chr9:30572382-30573180:-
Coord C1 exon
chr9:30573127-30573180
Coord A exon
chr9:30572472-30573126
Coord C2 exon
chr9:30572382-30572471
Length
655 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGAG
5' ss Score
6.38
3' ss Seq
TCGCATCTTGTTTTCCACAGGGA
3' ss Score
10.72
Exon sequences
Seq C1 exon
GGGTTGCCAGGAGAACATGGTATCCCTGGGAAACAAGGCGTTAAGGGAGAAAAG
Seq A exon
GTAGAGTGTAGATTTTATTTTTGTGTATTAAGTAAGTAGATAGAAACAAAACACAAAGGTCCTAATGTCGTAGAAGAAGCAAAAGATTACAAGGCTTGAGCCTCCCAGGATGTGTCAGTACAGGGGACAGACATTCAGACAAACTGTGTCATGGTGTCCCTGATGTCATGGCAGGGGTGGAGCGCAGAAACACCAGATAAGAAAATGAGCTAACCTAGAAGTGGAGATATTAGGGCTGAGGTCAAGCTCAGAAGTCTCGTAGTCTTTTACTGCCTGTTTCTTGACATGTCATATGCATATTAATATTTATACTGCACCACTCTCAGGAAATAATAAGGCATGTCGATCATCTAAAAGAGCTTCATGAATCGGCAGGCTCTTTGTTCCTGTGTTTGCGCGTTAGTCGGTGCTCCCTAGTACTGCTAAACTGTGTGTTGCAGACCTTGAGTCAGAACCTGAATGTGTCTAAGATATCAGGTAGAGCACTCAGAGTGAGCTAGGCACTTGGGAAATGCATCGGAGGGGCTGAATTTAGGACAGAATATAGGATAAGCTGATTGGCTATGACAACATAAAGCAACGGAAACTACTGTCTTCCCAATTCCCAAAATGAACTTCAGCAGAAAATGAAAGAATCGCATCTTGTTTTCCACAG
Seq C2 exon
GGAGATCCAGGAGGAAGGCTAGGCCCTCCTGGACTTCCAGGTCCGAAAGGTGATGCTGGGCCTCCAGGGAAAAGTCTGCCAGGGAAACCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000012759:ENSRNOT00000017169:24
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(0.1=0.0),PF0139113=Collagen=FE(27.9=100)
A:
NA
C2:
PF0139113=Collagen=PD(39.3=80.0),PF0139113=Collagen=PU(40.3=83.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
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]