BtaINT0106805 @ bosTau6
Intron Retention
Gene
ENSBTAG00000016849 | PABPC1L
Description
poly(A) binding protein, cytoplasmic 1-like [Source:HGNC Symbol;Acc:HGNC:15797]
Coordinates
chr13:74062442-74063223:+
Coord C1 exon
chr13:74062442-74062570
Coord A exon
chr13:74062571-74063116
Coord C2 exon
chr13:74063117-74063223
Length
546 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGT
5' ss Score
8.73
3' ss Seq
TCCCTACTTATTTCTTCCAGCCA
3' ss Score
7.63
Exon sequences
Seq C1 exon
CCGCTTACCCACCCGGGGCCTCGGTGGTCCGGCCAGCAGCCATGTCTCGGCGCCCCTTGACCCCCGTTGGAAGCTCCAGGCAGGTCTCCACCCACGTGCCACACCTGGTGCCCCACACCCAGCGAGTGG
Seq A exon
GTGAGTGTGGGCAGGGCCAAGAGGAACCGAATGGAGGGCAGGTGGGGGGGCAAGGGCTTGCTGCTGGGGTTGATGCTGGTGGGGAGTCAGAACCGGCCTCCACGGTGACCCTGCCGCTGGCCCCCTTGGAGGGCAGTGCTGGCACTGGAGACCTTGCACAGTAGTCAGTGGTAGTCAGCATGGGCTTCGGGGTCCTACAGACCTAGTTCTGGGGCTGACTCACTCTGATCTTGCCTGCTGCTGTACCTTGTATCCTCTTCCCTAAAATCCCGGTGAAAACAGTATGCCTGCTGTGTTATGTGAGTGAATGCAGTCATATCTGCAGGGGCTCAGCACCAGATCTGAATCTTAAGTACCTCAGCAGCTGTGAACAGGGGCATAGGTGCTGGCTATAAGGCCAGCATCTGTTCCTTCACCTGGCAGATGTTTGCACATCTGTGTGTTGACCCTTTACGCCGTTTAGGGAATTCAGTGTGAATGCTGGTTTTGAGCTGTTAGGCTTTTGAGTTGCTGTTGGGCCTTATCATCCCTACTTATTTCTTCCAG
Seq C2 exon
CCAACATTGGTACCCAGACCACAGGACCCAGTATGACGGGATGCTCTACCCCTAGCAGGCCTCTCCTGACACACACATACTCCACGCCAGCACACCGCACTGACAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000016849:ENSBTAT00000022412:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 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
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGCAGCCATGTCTCGGC
R:
CTGTCAGTGCGGTGTGCTG
Band lengths:
202-748
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development