HsaALTA0008955-2/2 @ hg19
Alternative 3'ss
Gene
ENSG00000124496 | TRERF1
Description
transcriptional regulating factor 1 [Source:HGNC Symbol;Acc:18273]
Coordinates
chr6:42200419-42204149:-
Coord C1 exon
chr6:42203943-42204149
Coord A exon
chr6:42200631-42200666
Coord C2 exon
chr6:42200419-42200630
Length
36 bp
Sequences
Splice sites
5' ss Seq
GCTGTAAGT
5' ss Score
8.56
3' ss Seq
AACCCTAATTTCCTTTTCAGGAC
3' ss Score
10.44
Exon sequences
Seq C1 exon
ACAAGTGAAGAAGAAGAAGAGTTAGAGGAGGAGGAGGAGGAGGACCCGGAAGAAGATAGGAAATCCACAAAAGAAGAAGAGAGTGAGGTGCCGAAGTCCCCGGAGCCACCACCCGTCCCCGTCCTGGCTCCCACGGAGGGGCCGCCCCTGCAGGCCCTGGGCCAGCCCTCAGGCTCCTTCATCTGTGAAATGCCCAACTGTGGGGCT
Seq A exon
GACTGTAGATGTCATGTCACTCCCTTTCTTCCCCAG
Seq C2 exon
GTGTTCAGCTCCCGACAGGCACTGAATGGCCATGCCCGCATCCACGGGGGCACCAACCAGGTGACCAAGGCCCGAGGTGCCATCCCCTCTGGGAAGCAGAAGCCTGGTGGCACCCAGAGTGGGTACTGTTCGGTAAAGAGCTCACCCTCTCACAGCACCACCAGCGGCGAGACAGACCCCACCACCATCTTCCCCTGCAAGGAGTGTGGCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000124496-22-23,22-22-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (No Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.783 A=NA C2=0.801
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCTCAGGCTCCTTCATCTGT
R:
GCCTTGGTCACCTGGTTGG
Band lengths:
113-149
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- The Cancer Genome Atlas (TCGA)
- Autistic and control brains
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)