RnoINT0040300 @ rn6
Intron Retention
Gene
ENSRNOG00000020579 | Col7a1
Description
collagen type VII alpha 1 chain [Source:RGD Symbol;Acc:1311417]
Coordinates
chr8:117720570-117720864:+
Coord C1 exon
chr8:117720570-117720626
Coord A exon
chr8:117720627-117720792
Coord C2 exon
chr8:117720793-117720864
Length
166 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGT
5' ss Score
11.01
3' ss Seq
TTTCTGACCTCTTGACCTAGGGT
3' ss Score
8.01
Exon sequences
Seq C1 exon
GGTGACTCAGCTGTGATTGAGGGACCTGCAGGGCCACGAGGTGCCAAGGGGGATATG
Seq A exon
GTAAGTGGGTGGGTCTGGTTCAGATATGAACTGGGTCTCCCTCGGCTATGGGAAAGAATTCTGTGGGGCTGGCCCAGGGGACCTGAGAGCTCAGCTTTCCAGAACAAAAGGGGCATCCAGCTCCTGACCCTGCCTCCTGACCCTGATTTCTGACCTCTTGACCTAG
Seq C2 exon
GGTGAACGAGGGCCTCGAGGCATAGATGGTGACCAAGGACCTCGGGGTGAAAGTGGGGATCCTGGGGACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020579:ENSRNOT00000027994:101
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(6.7=21.1),PF0139113=Collagen=PU(18.8=63.2)
A:
NA
C2:
PF0139113=Collagen=FE(35.9=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:
TCAGCTGTGATTGAGGGACCT
R:
TTGTCCCCAGGATCCCCACTT
Band lengths:
122-288
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]