RnoINT0039785 @ rn6
Intron Retention
Gene
ENSRNOG00000023972 | Col4a2
Description
collagen type IV alpha 2 chain [Source:RGD Symbol;Acc:1308085]
Coordinates
chr16:83392387-83392731:-
Coord C1 exon
chr16:83392570-83392731
Coord A exon
chr16:83392486-83392569
Coord C2 exon
chr16:83392387-83392485
Length
84 bp
Sequences
Splice sites
5' ss Seq
AAGGTACGG
5' ss Score
10.26
3' ss Seq
CTCTCCTGTCTTCATTGCAGGGC
3' ss Score
10.99
Exon sequences
Seq C1 exon
GCTACCAAGGCCCTCCAGGACCACCGGGGCCAAATGCACTTCCTGGAATCAAAGGAGATGAGGGGAGCTCGGGAGCTGCAGGTTTCCCCGGAGAGAAAGGATGGGTTGGTGACCCAGGGCCCCAGGGCCAGCCTGGTGTTCACGGTCTTCCAGGGGAGAAAG
Seq A exon
GTACGGTGAGGGGCCGGTACTGTGGGCAGGGGGCTGGAGAACCTATACGGTGCACTGGTCCTAACTCTCCTGTCTTCATTGCAG
Seq C2 exon
GGCCCAAGGGTGAGCAAGGATTCATGGGCAACACTGGGCCCTCTGGGGCCGTGGGTGACAGAGGCCCCAAAGGACCCAAAGGTGACCAAGGATTCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000023972:ENSRNOT00000057461:41
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PU(19.0=21.8)
A:
NA
C2:
PF0139113=Collagen=FE(52.4=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:
GGTTTCCCCGGAGAGAAAGGA
R:
GTCACCTTTGGGTCCTTTGGG
Band lengths:
168-252
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]