RnoINT0039939 @ rn6
Intron Retention
Gene
ENSRNOG00000056772 | Col4a6
Description
collagen type IV alpha 6 chain [Source:RGD Symbol;Acc:1589724]
Coordinates
chrX:112410980-112411704:-
Coord C1 exon
chrX:112411558-112411704
Coord A exon
chrX:112411097-112411557
Coord C2 exon
chrX:112410980-112411096
Length
461 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGA
5' ss Score
10.57
3' ss Seq
GTGCATTTTCTCTCTTACAGGTT
3' ss Score
12.55
Exon sequences
Seq C1 exon
GCTTTTCTGGCCCCCAGGGTGCTCCAGGACACACACCAATTGCTGAAGCTCGGCACGTTCCTCCAGGACCTTTGGGTCTGCCAGGCATTGATGGCATCCCAGGCCTCACAGGAGACCCTGGATCTCAAGGCTCTGTGGGTCTGCAAG
Seq A exon
GTAAGAATGACACCAGAAAAAGGGGACTCAGTGGGAAGCCAAAAGGCCTTGGTTCAGAGGCTAAAGCTACTGGATTGGCACAGTTCTGAGAAAGTGCCTTCATCAAACATTTCCCTAGCTACTTCCCAAGACTCCCAAACTCCTTGCCTGGGAAAGAAAAAGCTAGAAAGCCAATGGGACACTGGTTATACTTGTCTTCAGAGAACATGTGAATCTCTCCTCTAGACAGCTTGCCATTTCTAAAGTATTATTTGGAGCTAGAGGAGAAGGTGAGTAACAAAGGAGAACACAAGGTAGTAGAGAAAGCAAAGGCCTGGGGACAGAAAATATGGCTTTCAAGTCCTAGCTTTGCCCCAATAGGAGTAAGTTATTATTCTTCCTAGGACTTCTCATGAGTTTGAGGACACTCTGTGCCTTCCATATTGAGTGCTCCCCTACTCTGTGCATTTTCTCTCTTACAG
Seq C2 exon
GTTCCAAAGGCCTACCTGGCATCCCTGGCAAGGATGGCCCTAGTGGGCTTCCAGGCCCATCTGGAATCCTTGGTGATCCTGGTCTCCCTGGACTACAAGGACCTCCAGGATTTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000056772:ENSRNOT00000079180:39
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(18.3=22.0),PF0139113=Collagen=PU(54.2=64.0)
A:
NA
C2:
PF0139113=Collagen=PD(44.1=65.0),PF0139113=Collagen=PU(60.0=90.0)
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:
GTGCTCCAGGACACACACCAA
R:
CTTCAAATCCTGGAGGTCCTTGT
Band lengths:
246-707
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]