RnoINT0040342 @ rn6
Intron Retention
Gene
ENSRNOG00000020579 | Col7a1
Description
collagen type VII alpha 1 chain [Source:RGD Symbol;Acc:1311417]
Coordinates
chr8:117705665-117705927:+
Coord C1 exon
chr8:117705665-117705700
Coord A exon
chr8:117705701-117705855
Coord C2 exon
chr8:117705856-117705927
Length
155 bp
Sequences
Splice sites
5' ss Seq
CCGGTAGGT
5' ss Score
9.39
3' ss Seq
TGCTTTTTGCCCCCACACAGGGG
3' ss Score
8.51
Exon sequences
Seq C1 exon
GGAGAACGAGGGCCTCAAGGCCCAAAAGGGGAGCCG
Seq A exon
GTAGGTGAAAGGGAAACGGGGCCAGGATATTCCCTGGAGTGGGGGTGCCCCAGGCCAGACCCTGTACAAGACCTGAAGCATGCTAAGAACTGGAGCACCACCAAGGGCTTCTTCCACCTTCCCTACCCTAAGAACTGCTTTTTGCCCCCACACAG
Seq C2 exon
GGGGAGCCTGGGCAAGTCATTGGAGGCGGAAGGCCAGGGCTTCCTGGAAAGAAAGGGGACCCTGGACCTTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020579:ENSRNOT00000027994:34
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(17.7=100)
A:
NA
C2:
PF0139113=Collagen=PD(11.3=29.2),PF0139113=Collagen=PU(28.8=70.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGAGAACGAGGGCCTCAAGG
R:
GAAGGTCCAGGGTCCCCTTTC
Band lengths:
107-262
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]