BtaINT0106817 @ bosTau6
Intron Retention
Gene
ENSBTAG00000016849 | PABPC1L
Description
poly(A) binding protein, cytoplasmic 1-like [Source:HGNC Symbol;Acc:HGNC:15797]
Coordinates
chr13:74061726-74062570:+
Coord C1 exon
chr13:74061726-74061810
Coord A exon
chr13:74061811-74062441
Coord C2 exon
chr13:74062442-74062570
Length
631 bp
Sequences
Splice sites
5' ss Seq
CATGTGAGT
5' ss Score
7.83
3' ss Seq
CATGTTCCCCGTGCCACAAGCCG
3' ss Score
2.26
Exon sequences
Seq C1 exon
CCTCCAGCTCAGGCTCCCTACTATGGCTCTGGCCCACCCATCCAGCCTGCCCCCAGGTGGACGGCCCAGCCACCCAGACCGTCAT
Seq A exon
GTGAGTGACCCAGCCCCTCCCCCTCGTGCCCCACCCCCGGGGGGGCAGCATGTGTTAAAGATGTGGACTTGGGGGTCAAGCCTGGCTCTGCTGCTTCCTAATCATTTGGGTGGGTGACGTCTCCCCTCTGAGCCTTGGTTTCCTCTTGTGAACATGAGCCTGAGTGAGATGAGTGTAAAACACCAAGGACAGGGCTGTGTGTGTGTAGAAGACACGCACACAGGAGCTGTTACCTTCAGTGAGCTCCAAAGGCTCTCTGGACTGGTGGTGGTGAAAGTTCCTGCAAAGCTGAGAAAACGAAACTCCACTGGCAGTACTGTTGAGGATGGTCCTTCTCTTCAGAGGGAAGTTCACCCTGACCTGAAGCTGACTTTGGGGGGCCAGGGTGTGTGGTCCTGATACCTATGCCTCTTGGGGTCCCGGGTAGACAGAAGTCGGGTTGGCTTTTTAATTGCAGATTTCCATCCCCCTCCCCTGGAGGTCTGGGTCTCCGGTGAATTCCCTCCCTCCTTTGTCTGCCATTCATGTTCACCTTGCCACCCGCTTCCTCACCTTGGAACTGTCAGGGTGCAGTGTGTCCCTCTGATTTTCCCCCTCCACTAAACTTTCTCCATGTTCCCCGTGCCACAAG
Seq C2 exon
CCGCTTACCCACCCGGGGCCTCGGTGGTCCGGCCAGCAGCCATGTCTCGGCGCCCCTTGACCCCCGTTGGAAGCTCCAGGCAGGTCTCCACCCACGTGCCACACCTGGTGCCCCACACCCAGCGAGTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000016849:ENSBTAT00000022412:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.862 A=NA C2=1.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCAGGCTCCCTACTATGGCT
R:
CACTCGCTGGGTGTGGGG
Band lengths:
206-837
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development