RnoALTD0007416-2/2 @ rn6
Alternative 5'ss
Gene
ENSRNOG00000010663 | Col6a5
Description
collagen type VI alpha 5 chain [Source:RGD Symbol;Acc:1565804]
Coordinates
chr8:114595364-114598203:-
Coord C1 exon
chr8:114597628-114598203
Coord A exon
chr8:114597307-114597627
Coord C2 exon
chr8:114595364-114595704
Length
321 bp
Sequences
Splice sites
5' ss Seq
GATGTAAGG
5' ss Score
6.35
3' ss Seq
CTTGTTTCTTTGGTCTCCAGATT
3' ss Score
8.68
Exon sequences
Seq C1 exon
CATGACAACTTTCTTGTCAGACTTAATTGATAATTTTGACATTGAGTCTCAAAGACTGAAAATCGGGATGGCTCAGTACGGGAGCCGGTATCAGGAAATTATTGAGTTGGAAAGCTCTCTGAACAAAACTCAGTGGAAATCTCAGGTCCACAGTGTGGCTAAGAGCAAGGGGCTTCCACGAATTGACTTTGCTCTTAAGCATGTGAGTGACATGTTCGACCCTTCGGTTGGCGGGAGAGGAAACGCTGGTGTCCCTCAGACTTTGGTTGTTATAACATCTAGTTATCCGCACTATGATGTGTCAAGAGCAGTGAAGGTCCTGAGAGAACTTGGCATCTGTATCCTGGCTTTGGGAATAGGAAATGTTTATAAGGGACAGCTTCTGCCCATCACAGGCAATTCAGAAAAAATAATTACGTTCAAAGACTTTAATACACTAAAGAATGTGGACGTGAAGAAAAGAATGGTCCGTGAAATTTGCCAGAGCTGCGGGAAAGCCA
Seq A exon
GTGAGTGTCTCGCCGTTGTTTGGTTTTATTAGAGGCTTCCTGTGCCCTTGTTTCCGAAGGTTGTATTATGGGCCGGCCCCTTTGGAATCCATTTAGGACAATGTGTGGTGAGAAGAGATGTTGATTGTTGCTTCTCCCTGGAAGCTTGGGCTTAGTCAGCCTTCCTCAGTGGCAGGATTGGTACAGAGCATAAGGGGATGGGATTGGCTGTGTCCTGTAGGCATCCCCATCCTCTCACTACAACCAGTTTCTCCTCCTTTCATACACGGAGCTCTGTGTCCTGTACAAGTCCTCTAGACTATGCTCTTCATCTGATTGGAT
Seq C2 exon
ATTGCTTTGTGGATGTAGTGGTCGGGTTCGACATTTCCACTCACCGTCAGGGCCAGTCTTTGTTCCAGGGCCATCCCCGCTTGGAATCGTACCTCCCAGGCATCTTGGAGGACATCACCTCTATCAGAGGGGTGAGCTGTGGTGCAGGAGCAGACACACAGGTGAGCTTGGCCTTTAAGGTGAACAGTGAGCAAGAGTTCCCAGCCAAGTTCCAGATCTATCAGAAAGCAGCGTTCAACAGCTTGTTGCAAGTCACCGTCCGTGGACCAACTCATCTGAATGCACAGTTCTTACAGTCACTCTGGGATGTGTTTGAGGAAAGATCTTCATCCAGGGGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000010663-8-6,9-6-2/2
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
ORF disruption when splice site is used (sequence inclusion)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0009223=VWA=WD(100=90.2)
A:
NA
C2:
PF057629=VWA_CoxE=PU(44.4=35.1)
Main Inclusion Isoform:
NA
Other Inclusion 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:
TGGTGTCCCTCAGACTTTGGT
R:
GTACGATTCCAAGCGGGGATG
Band lengths:
346-667
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]