RnoALTD0007414-2/2 @ rn6
Alternative 5'ss
Gene
ENSRNOG00000010663 | Col6a5
Description
collagen type VI alpha 5 chain [Source:RGD Symbol;Acc:1565804]
Coordinates
chr8:114533343-114543947:-
Coord C1 exon
chr8:114543844-114543947
Coord A exon
chr8:114543739-114543843
Coord C2 exon
chr8:114533343-114534029
Length
105 bp
Sequences
Splice sites
5' ss Seq
CCGGTAAGA
5' ss Score
10.1
3' ss Seq
CTAAAGTTACTCTGTTGCAGAAC
3' ss Score
5.36
Exon sequences
Seq C1 exon
ATTGACGGCCAAGCTGCATGAGGTTTCTGCGAGCAAGAACAGTCCGGCTGGTCAAGAGCTGAAAGCCAGGAAAGACTTGTCTGTAGTGTTGGAGGATCACGGAG
Seq A exon
GTGACCATTTGGTTTACATTCCAACCCATATGGTAGAGCCACATAAGTTAGCGAGTCACTATGGAAATGACCAGGAGTCTGTTAGAATGGCAAGCCTCACTTCCG
Seq C2 exon
AACATGAAAATCATAGCAGAAGAGAACTGAGTCTTGCTCAAGAGCCTGGAGATGCTTCTCCTCAAGAATATTACATGGATGTGGCTTTCCTCATAGATGCTTCTCAACAAATAGGACATAATGCGTTTACAGAAGTGAGAGCTTTTATAACTTCAGTACTAGATTACTTTCACATCACCCCAGCTCCACTGACCTCTGTCTTAGGAGACAGAGTGGCTGTCCTGACCTATTCTCCTCCAGGCTATCTGCCAAACACGGAAGAATGCCCAGTCTACCTGGAATTCGATTTGGTCACTTACAACACTGTACACCAAATGAAGCGTCATCTCCAAGAGTCTCTTAAGCAACTCAATGGAGATGTTTTTCTTGGGCATGCCCTTCAGTGGACAATTGACAATGTCTTTGTAGGAACACCCAATCTGAGGAAAAACAAAGTTATCTTTATAGTAACTGCAGGGGAAACCAACCCGTTAGACAAAGAAGTTTTAAGGAATGCATCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000010663-45-41,46-41-2/2
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.451 A=NA C2=0.074
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0009223=VWA=WD(100=80.4)
Main Skipping Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg19)
No conservation detected
Mouse
(mm9)
No conservation detected
Cow
(bosTau6)
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:
GGTCAAGAGCTGAAAGCCAGG
R:
GGAGCTGGGGTGATGTGAAAG
Band lengths:
242-347
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]