BtaINT0106812 @ bosTau6
Intron Retention
Gene
ENSBTAG00000016849 | PABPC1L
Description
poly(A) binding protein, cytoplasmic 1-like [Source:HGNC Symbol;Acc:HGNC:15797]
Coordinates
chr13:74052755-74053142:+
Coord C1 exon
chr13:74052755-74052894
Coord A exon
chr13:74052895-74053047
Coord C2 exon
chr13:74053048-74053142
Length
153 bp
Sequences
Splice sites
5' ss Seq
TTGGTGGGC
5' ss Score
3.03
3' ss Seq
AGCCGAGTTGCCCTTCCCAGGGA
3' ss Score
3.62
Exon sequences
Seq C1 exon
CTTCGTTGGCCACTTCAAGTCCCGACGGGAGCGGGAGGTGGAGCTGGGCGCTCGGGCCATGGAGTTCACCAACATCTACGTGAAGAACCTCCACGTGGACGTGGATGAGCAGCGCCTGCAGGACCTCTTCTCCCAGTTTG
Seq A exon
GTGGGCGAGTTTCCCAAGGGAGTTGAGGATCACTTCTACTCCCAGCTCAGGCTGTGGGGAGGGCCCCCTGGGGCTTCCAGAAGGCTTTGGGGGAGGGTGGGGGACATTTCGAGGCTTCCTTGACACCCCTTTGAGCCGAGTTGCCCTTCCCAG
Seq C2 exon
GGAAGATGCTGAGTGTCAAGGTGATGAGGGATGACAGTGGCCACTCCCGCGGCTTTGGCTTTGTCAACTTCGAGAAGCATGAGGAAGCCCAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000016849:ENSBTAT00000022412:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=PD(1.4=2.1),PF0007617=RRM_1=PU(31.4=45.8)
A:
NA
C2:
PF0007617=RRM_1=FE(44.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTCGTTGGCCACTTCAAGTCC
R:
CTTCTGGGCTTCCTCATGCTT
Band lengths:
234-387
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development