RnoALTA0001062-2/2 @ rn6
Alternative 3'ss
Gene
ENSRNOG00000019648 | AABR07068316.1
Description
collagen type VI alpha 3 chain [Source:NCBI gene;Acc:367313]
Coordinates
chr9:97938181-97940124:-
Coord C1 exon
chr9:97939426-97940124
Coord A exon
chr9:97938284-97938306
Coord C2 exon
chr9:97938181-97938283
Length
23 bp
Sequences
Splice sites
5' ss Seq
GCAGTAAGT
5' ss Score
9.07
3' ss Seq
TCCATATGATTCACATAAAGTTT
3' ss Score
1.73
Exon sequences
Seq C1 exon
CAAGGCTTCCCAGCACTTTGCCAGGGTGGCTGTTGTGCAGCAGGCCACCTATGAGTCCGTGGACAACACCAGTGTGCCACCAGTGAAGGTGGAGTTCTCACTGACAGACTATGGTGCCAAGGAAAAGCTGCTAGACTTCCTTAGCCGGAGGATGACCCAACTTCAGGGAACCATGGACCTGGGCAATGCCATTGAATACACTATAGAGAACATCTTTGAAAGTGCTCCAAACCCACGGGACCTCAAAATTGTGGTGCTGATGCTGACCGGGGAGATACCAAGGGAGCAGCTGGAGGAGGCCCAGAGAGCCATCCTCCAGGCCAAGTGCAAGGGTTACTTCTTCGTGGTTCTGGGCATTGGCAGGAAGGTGAACGTCAAGGAGGTCTACAGTTTTGCCAGTGAGCCCAATGATGTCTTCTTCAAATTCATGGACAAATCGACTGAGCTCAACGAGGAGCCTCTGATGCGCTTTGGAAGGCTGCTCCCTTCCTTTGTCGGCA
Seq A exon
TTTGATTTTTTTTCCCCCTCTAG
Seq C2 exon
GTGGAAATGCATTTTACCTGCCTCCAGATCTCAGGAAGCAGTGTGATTGGTTCCAAGGGGACCAACCAGTGAAGAATGGCGTGAAGTTTGGTCACAGACAGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000019648-45-44,45-43-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
NonCoding
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=NA
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NA
Main Inclusion Isoform:
NA
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:
ATCGACTGAGCTCAACGAGGA
R:
TTCCTGAGATCTGGAGGCAGG
Band lengths:
102-125
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]