BtaALTA0026120-2/2 @ bosTau6
Alternative 3'ss
Gene
ENSBTAG00000005844 | SCAMP2
Description
Bos taurus secretory carrier membrane protein 2 (SCAMP2), mRNA. [Source:RefSeq mRNA;Acc:NM_001102170]
Coordinates
chr21:34219003-34219763:+
Coord C1 exon
chr21:34219003-34219101
Coord A exon
chr21:34219635-34219645
Coord C2 exon
chr21:34219646-34219763
Length
11 bp
Sequences
Splice sites
5' ss Seq
CAGGTACCG
5' ss Score
10.05
3' ss Seq
AGTGGAGCTGTGTGTTGCAGCTC
3' ss Score
3.61
Exon sequences
Seq C1 exon
ACAAATGCAGCGACGACGGTTCCTGTCTCACAGATGCCCGGGGCCTCGCAGCCGGCAGTTCTCCAACCCTCAGTGGAGCCCACCCAGCCAACCCCCCAG
Seq A exon
CTCCTGCTTAG
Seq C2 exon
ACAGGCCAGCAGGTTCCTGCCCACCAGATTCCTGGCAGTGAGTGAGCTCTCAGAGAGGCAGATGCTGCTAGGAGGAGATAGTATTCTCAGAGACAGCTACCTGCGAAACCTGCCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000005844-7-7,7-6-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (No Ref, Alt. Stop)
No structure available
Features
Disorder rate (Iupred):
C1=0.990 A=NA C2=0.070
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Mouse
(mm10)
No conservation detected
Rat
(rn6)
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:
GCAGTTCTCCAACCCTCAGTG
R:
GCTCACTCACTGCCAGGAATC
Band lengths:
92-103
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development