BtaALTA0021018-2/2 @ bosTau6
Alternative 3'ss
Gene
ENSBTAG00000016849 | PABPC1L
Description
poly(A) binding protein, cytoplasmic 1-like [Source:HGNC Symbol;Acc:HGNC:15797]
Coordinates
chr13:74055918-74060687:+
Coord C1 exon
chr13:74055918-74056013
Coord A exon
chr13:74060421-74060478
Coord C2 exon
chr13:74060479-74060687
Length
58 bp
Sequences
Splice sites
5' ss Seq
AAGGTCAGG
5' ss Score
6.23
3' ss Seq
TTGTCTTGTCTTGCTTTTAGGTG
3' ss Score
11.3
Exon sequences
Seq C1 exon
GGCGTGAACTTGTATGTGAAGAACCTGGATGACTCCATAGATGATGAGAAACTGAGGAAAGAGTTCTCTCCCTATGGAGTGATCACCAGTGCCAAG
Seq A exon
GTGATGACAGAGGGTGGCCACAGCAAAGGGTTTGGCTTTGTGTGTTTTTCCTCTCCAG
Seq C2 exon
AAGAGGCGACCAAGGCCGTGACAGAGATGAACGGGCGCATCGTGGGCACCAAGCCACTGTACGTGGCGCTGGCCCAGCGCAAGGAAGAGCGGAAGGCCATCCTGACCAACCAGTACATGCAGCGCCTCTCCACCATGCGGGCCCTGGGTGGCCCCATCCTGGGCTCCTTCCAGCAGCCTGCCAGCTACTTCCTGCCCGCTGTGCCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000016849-8-8,8-7-2/2
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=0.090
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=PU(40.6=87.5)
A:
NA
C2:
PF0007617=RRM_1=PD(56.5=43.8)
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGAGTGATCACCAGTGCCAAG
R:
GCTGCATGTACTGGTTGGTCA
Band lengths:
144-202
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development