BtaALTA0031200-2/2 @ bosTau6
Alternative 3'ss
Gene
ENSBTAG00000015321 | TRERF1
Description
transcriptional regulating factor 1 [Source:HGNC Symbol;Acc:HGNC:18273]
Coordinates
chr23:15982902-15984368:-
Coord C1 exon
chr23:15984215-15984368
Coord A exon
chr23:15983013-15983147
Coord C2 exon
chr23:15982902-15983012
Length
135 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
AGCCTTTATTGTCTGTGTAGGAG
3' ss Score
6.4
Exon sequences
Seq C1 exon
CAGTGGCCAACCCAAAGGAGTGTTTGGGGAGCAGTTTGATGCCAAGAACAAGCTGACATGCTCCATCTGCCTGAAGGAGTTCAAGAGCCTGCCCGCCCTGAATGGCCACATGCGGTCCCATGGGGGGATGAGGGCCTCCCCCAGCCTCAAACAG
Seq A exon
GAGGAAGGAGAGAAGGCCCCGGCGCCTCCGCCTCAGCCCCAGCCGCCACTGCCGCCTCCGCCGCCGCCACCTCAGCTCCCTCCCGAGGCGGAAAGCCTCACGCCTATGGTCATGCCCGTGTCTGTCCCTGTCAAG
Seq C2 exon
CTTCTCCCGCCCAAGCCCAGCTCTCAGGGCTTCGCCAACAGCGTCGCTGCCGCCCCCTCGGCCAGAGACAAGCCAGCCAGCTCGATGTCGGACGACGAGATGCCCGTGCTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000015321-3-4,3-3-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.654 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF139121=zf-C2H2_6=WD(100=46.2)
A:
NA
C2:
NO
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm10)
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:
CAAAGGAGTGTTTGGGGAGCA
R:
ATCTCGTCGTCCGACATCGAG
Band lengths:
243-378
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development