BtaALTA0007797-2/2 @ bosTau6
Alternative 3'ss
Gene
ENSBTAG00000030190 | COL6A3
Description
collagen, type VI, alpha 3 [Source:HGNC Symbol;Acc:HGNC:2213]
Coordinates
chr3:117427718-117429713:-
Coord C1 exon
chr3:117429015-117429713
Coord A exon
chr3:117427794-117427820
Coord C2 exon
chr3:117427718-117427793
Length
27 bp
Sequences
Splice sites
5' ss Seq
GCAGTGAGT
5' ss Score
7.39
3' ss Seq
AAATTTTTTTTTCCCTCTAGGTA
3' ss Score
11.65
Exon sequences
Seq C1 exon
CAAGGCCTCCCAGCACTTTGCCCGCGTGGCGGTGGTGCAGCATGCGCCCTACGAGGCGGTGGACAACGCCAGTGTGCCGCCTGTGAAGGTGGAGTTCTCCCTGACCGACTACGGCTCCAAAGAGAAGCTGCTGGCCTTCCTTGGCAGCAGGATGACCCAGCTGCAGGGGACCAGGGCTTTGGGCCGCGCCATCGACTACACCATTGAGAACATCTTCGAAAGTGCTCCCAACCCCCGGGACCTGAAGATCGTGGTGCTGATGCTGACGGGCGAGGTGCAGAAGCAGCAGCTGGAGGAGGCCCAGAGAGCCATCCTACAGGCCAAGTGCAAAGGCTACTTCTTCGTGATCCTGGGCATTGGCAGGAAGGTGAATGTCAAGGAGCTGTACAGCTCTGCCAGCGAGCCCAACGACGTCTTCTTCAAGCTAGTGGACAAGTCGACCGAGCTCAACGAGGAGCCCCTAATGCGCTTCGGGAGGCTGCTGCCATCCTTCGTCAGCA
Seq A exon
GTAAAGATGCTTTCTACCTGTCCCCAG
Seq C2 exon
ATATCAGGAAACAGTGTGATTGGTTCCAAGCAGACCAACCGGCAAAGAATCTCGTGCAGTTTGGTTACAAACAAAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000030190-43-48,43-47-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0009223=VWA=WD(100=82.1)
A:
NA
C2:
NO
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GACAAGTCGACCGAGCTCAAC
R:
CGAGATTCTTTGCCGGTTGGT
Band lengths:
124-151
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development