BtaALTA0005282-2/3 @ bosTau6
Alternative 3'ss
Gene
ENSBTAG00000023776 | C9orf116
Description
chromosome 9 open reading frame 116 [Source:HGNC Symbol;Acc:HGNC:28435]
Coordinates
chr11:106452557-106455940:+
Coord C1 exon
chr11:106452557-106452635
Coord A exon
chr11:106455538-106455540
Coord C2 exon
chr11:106455541-106455940
Length
3 bp
Sequences
Splice sites
5' ss Seq
CCGGTAAGG
5' ss Score
10.19
3' ss Seq
TGTCCCCTTCTCACTTCCAGAAG
3' ss Score
10.81
Exon sequences
Seq C1 exon
GACCAAGGAGCCCCCCTCAGTGTACAGGACCAGTAACCAAGCTTATGGTAGCAGAGCCCCCACTGTGCACGAGATGCCG
Seq A exon
AAG
Seq C2 exon
GTGTTTTATCCAAATTCGTATAAGTTTTCTAGACAAGTTGCAGTGGGCGGAATGTTCCAGAACAACACGCTCAATGTCTACATGGAGAAGAGCATTGTGACAGGTCCTGACAACTACATCACCTCCTATGACCGGCTCAACTTCCACCCCAGCTACAGGGTCTGCAGGCCGTCCATCTGTGACTGAGGGGCCTCCCGGCTCCTCTGGACGGCTGTCCACCCTAGTCCTCGATGGTTCGCCCAGGCGTAAAGGGACGCACTTGGCCACTTTTCCCGAAAACACTTTTCCTTTCTAGATAAGCAGGCAGACGGGGCGGCGATGCTCTGCTTTCTCTGTTTTACGCCTGAGACGAAAAAGAGCTGATGGCTTGACTTTCCATTAAAACTCTTGCCACGGCCTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000023776-1-5,1-4,1-3-2/3
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.481 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF148921=DUF4490=FE(24.3=100)
A:
NA
C2:
PF148921=DUF4490=PD(29.9=50.8)
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:
CCAAGCTTATGGTAGCAGAGCC
R:
CGCCCACTGCAACTTGTCTAG
Band lengths:
92-95
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development