RnoALTA0009891-1/2 @ rn6
Alternative 3'ss
Gene
ENSRNOG00000020579 | Col7a1
Description
collagen type VII alpha 1 chain [Source:RGD Symbol;Acc:1311417]
Coordinates
chr8:117699390-117700172:+
Coord C1 exon
chr8:117699390-117699533
Coord A exon
NA
Coord C2 exon
chr8:117700053-117700172
Length
0 bp
Sequences
Splice sites
5' ss Seq
CTGGTCAGA
5' ss Score
3.96
3' ss Seq
CCCGTTATCTCCCTCTCCAGATC
3' ss Score
11.56
Exon sequences
Seq C1 exon
GTCCAGAGTCCAGTCAGACGCTGGCCCCAGACTCTACTGTCACAGACATCCTGGGGCTGCAGCCTGGAACCTCTTATCAAGTGGCTGTGTCAGCCCTTCGAGGGAGAGAAGAGGGGCCCCCTGTGGTCATCGTGGCTCGAACTG
Seq A exon
NA
Seq C2 exon
ATCCACTGGGCCCAGTGAGGAGAGTCCACTTGACTCAGGCTGGTAGCTCATCTGTCAGCATTACCTGGACTGGGGTTCCTGGCGCCACCGGATACAGGGTTTCCTGGCACTCAGGCCATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020579-18-17,18-16-1/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.551 A=NA C2=0.293
Domain overlap (PFAM):
C1:
PF0004116=fn3=PD(53.2=83.7)
A:
NA
C2:
PF0004116=fn3=PU(46.8=90.2)
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCCAGAGTCCAGTCAGACGC
R:
CTGAGTGCCAGGAAACCCT
Band lengths:
257-579
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]