RnoINT0039937 @ rn6
Intron Retention
Gene
ENSRNOG00000056772 | Col4a6
Description
collagen type IV alpha 6 chain [Source:RGD Symbol;Acc:1589724]
Coordinates
chrX:112413512-112413923:-
Coord C1 exon
chrX:112413762-112413923
Coord A exon
chrX:112413611-112413761
Coord C2 exon
chrX:112413512-112413610
Length
151 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGT
5' ss Score
11
3' ss Seq
TTTCCTTTGGCCCTTACCAGGCA
3' ss Score
8.31
Exon sequences
Seq C1 exon
GCCGCCCAGGTCTCCCAGGCCCTCCAGGTCCCCCTGGACCATCCTCAGATCAAGGCGATCCTGGAGACTCTGGCTTCCCTGGAATTCCAGGCCTTCAAGGGCTCAAGGGAAACCAGGGACTTCCGGGTTTCTCTGGGCTCTCTGGAGATCTAGGGCTAAAAG
Seq A exon
GTAAGTCTGTTCCACCAGCTGCAAGACCTATCAGTCACCACTGTATAGTCCAGTTGCCGTGAAGAGGTTCATGAATGGTGCTTTTCCTGACCAATCTCCCTCTGTCACCATCATGGCAACACCTGACATGTTTTCCTTTGGCCCTTACCAG
Seq C2 exon
GCATGAGAGGGGAACCTGGCCTCATGGGGACTCCTGGCAAGATTGGGCCACCAGGAGACCCAGGATTTCCTGGAATGAAGGGGAAGGCGGGGCCAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000056772:ENSRNOT00000079180:37
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(71.4=81.8),PF0139113=Collagen=PU(25.0=27.3)
A:
NA
C2:
PF0139113=Collagen=FE(55.0=100)
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:
CAGGTCTCCCAGGCCCTC
R:
GCCTTCCCCTTCATTCCAGGA
Band lengths:
244-395
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]