RnoINT0039556 @ rn6
Intron Retention
Gene
ENSRNOG00000007657 | Col27a1
Description
collagen type XXVII alpha 1 chain [Source:RGD Symbol;Acc:735115]
Coordinates
chr5:79162160-79162475:+
Coord C1 exon
chr5:79162160-79162177
Coord A exon
chr5:79162178-79162439
Coord C2 exon
chr5:79162440-79162475
Length
262 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGT
5' ss Score
10.45
3' ss Seq
GTTTCCTCTTTCTCCCACAGGGT
3' ss Score
13.08
Exon sequences
Seq C1 exon
GGACTGCAAGGCCCAAGG
Seq A exon
GTAAGTAGGGTGGGTGTGAAGACTTGAGACTGCGGACAGGAACTGGGGGAGGAGGCTCTCAGATCTTCCCCTCCTCCCTCCCTCCCTCCTCCCTCCCTCCCTCCCTCCCTTCCTCCCTCCTCCCTCCTTCTTCCCCTCCCCCCTCTCTGGCATTCCTCCCCATTGTTTACTTTTTTTCCCAGGGGAACATCATCTCTGGGCCTGGGAAGACACCCTGGGTAAAGAGCTGTCAAGAGCTGACTGTTTCCTCTTTCTCCCACAG
Seq C2 exon
GGTCCTCCTGGTCCGAGGGGGCGGCCAGGTCCACCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000007657:ENSRNOT00000010333:54
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=FE(7.9=100)
A:
NA
C2:
PF0139113=Collagen=FE(17.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg19)
No conservation detected
Chicken
(galGal4)
No conservation detected
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]