HsaALTD1036244-2/3 @ hg38
Alternative 5'ss
Gene
ENSG00000172752 | COL6A5
Description
collagen type VI alpha 5 chain [Source:HGNC Symbol;Acc:HGNC:26674]
Coordinates
chr3:130443484-130455666:+
Coord C1 exon
chr3:130443484-130449939
Coord A exon
chr3:130449940-130449987
Coord C2 exon
chr3:130455455-130455666
Length
48 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGTA
5' ss Score
5.89
3' ss Seq
AAAGTTTTTTTTTCTTCTAGATT
3' ss Score
8.68
Exon sequences
Seq C1 exon
GATATAGGGCTGAATTGTGCCCTTTTGACCATCAGGGCCAGTGCAAGGCAAGATAAATGTGCTCTCATAAACTTCCTCAGCCTTTCCAACACCTACTAGTCCCATGTTAGCGGGATGTTTAAGCCAAGAGGAAGGCCATAAACTAGAGGAAATAACAGAAACATCAGCACCAGTATCTACTAGGCCCTCAGACTTTTTTCCTCGAATGTGTATGGTGCACGTGGGCCTTTGTTTAGAAATTACATTAATCCAATAAGCGGCCTTTTCACCGCCGGAGCCCATCCCAGGGCCACGTGCCTTATCTCCTTTGTTTAAAACGGTATTAGGTAGTAAAAGCAATTGAGCAATTGACTCACCGGCCAGAATGGAAACAGGAACCTTGGCAGACACGATTAATTTAATCTCATCAACGGAATCAGAATTAATGAGACCAGTATGAATGGTGATTCCTTTAGCAGAGGTAGATGCTCTACCTAACACCAGGCCCACCGAACCTTGAG
Seq A exon
GTAAAGGGCCAGTGACCCCCGTGGGGACAATCAAAGGCAAAGAATCAG
Seq C2 exon
ATTTGTTACTGAGCTACAAGAGGATTTTTTGGGAGGTAATGGCTTCATTGGCCAAGAATTAAATTCTGGGAGAGAATCACCTTTTGTAAAGACGGAAGACAATGGAAGTGACTATTTGGTTTACCTTCCAAGCCAAATGTTTGAGCCACAAAAATTAATGATCAATTATGAAAAAGATCAAAAATCTGCAGAAATTGCAAGTCTCACTTCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000172752-46-46,47-46,48-46-2/3
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
In the CDS, with uncertain impact
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.131
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
Rat
(rn6)
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:
CTCTACCTAACACCAGGCCCA
R:
AGTCACTTCCATTGTCTTCCGT
Band lengths:
146-194
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains