BtaINT0106807 @ bosTau6
Intron Retention
Gene
ENSBTAG00000016849 | PABPC1L
Description
poly(A) binding protein, cytoplasmic 1-like [Source:HGNC Symbol;Acc:HGNC:15797]
Coordinates
chr13:74064246-74065903:+
Coord C1 exon
chr13:74064246-74064339
Coord A exon
chr13:74064340-74065772
Coord C2 exon
chr13:74065773-74065903
Length
1433 bp
Sequences
Splice sites
5' ss Seq
TCGGTGAGT
5' ss Score
11.11
3' ss Seq
TCAGAGGCTGTTCTATACAGGTG
3' ss Score
4.4
Exon sequences
Seq C1 exon
GTCCAGGAGCCCGCTGTGCACGTCCCCGGACAGGAGCCCCTGACCGCGTCCATGCTGGCTGCAGCACCGCTGCACGAGCAGAAGCAGATGATCG
Seq A exon
GTGAGTGGCTGTTTCCCCTACCCTGGAGCAGGAGGGGGGTGCACCACCAGCTGACTCACCAGCTGGAGGTCAGATGTGGAGACCAGGTCCCCAGCCTCAAGCTGACCCACCTGCTGGGTGACCTTGTCCAAAGTGCCTTTACTTCCCAGGCTCCTGTTCATCTTCAAACACTGGTCAGACCAGGCAGTCCGAGATTTCTTCCAGCCTCGCTGTTCAGTGACTTTGACTCCGGCTGGGAGAAACCCCAGATGTGGGGAGATGGGTGAGGGGAGCTCGAGGGGGTAGGAGGAGGAGCAGGAGGGTAGGGTCTTGGGTTTCTGCCAGCAGATGCCTGTAGGGTGGGTGCTGTGGTTCCACACACCCCTCCTGTCGGGAAGAGGCTGTCACCACGTTTCATCAGTCACCCAGCGCCCACTGCTGGGAGGCAGGATATAAACATGCACTGGGGAAATACACGGTCCCCCACACCTGAACTCCTGCGCACGCATCTCCTTCCCGGTGTCTGGCAGGCCCTGCTGAAGGGTTAGGGTTAGGGTTAATTAAAAGAATGAATGAATGAACGAGCTCGCCATGGTCTCCAGGCTCTCTTCACCAAGACCTCCAGGCTCTTCTCTGAAGGCCCCCAATGCCGTCAGCCCATCGTTTACCCAGCTCACTGGGGCTTCTGTCACTTTCCTACCCACCCCTCAAAGAAAAACTGTAAATGGGCTTCATGGAGGGGGAAGGCTCTGTGGGCAGTGCCCTGGAGACTCCTTCACTCTCCTCGTGGGAGAAGCCCTCCCGCCCCCACTAATGGCACCTAGCGCCCTGTTCTGGCTACACCCTCCACGCATCGCCACCAGCACGAGGCCCCATCCCTGGAAGTGCCCGCTGGTGGAAGGTGAATTTATCTTGTGTGTTTGGCTCCACCATCCCTCCAAAAAATCAAGTTCCACATTATTGTATCCTGTCTAGAATTCCATGTGATCCTTCAAATGACTTCTTGCCCAATGAACAAGAGTAGTTTGGTTTTTTTCCCTGCCATACCATGAGGCATGTGAGATCTTAGTGCCCCGAGCAGGGATCAAACCCTGCCCCCTGCATTGGAAGCACAGAGTCTTAACCACTGGAGTGCAAGGGAAATCCAGCAAGAGTAGTCTTTAAACTGCAATCAAGGCTGTGCCAGATCACCTATGCAGTATAACGTATAATGTCAAATTTGATTCTTCAAACCAGCCTCCAAGGTGGGGCTTGCTGTGCTCACTTTACACTTGGGGAAGAGGCTCCTAAGAAGGTTCAGTGACACACCTGGAGGAAGCCGTCCTGGGGCGGAAACCTGAAATGCCTCTCTGTTCAGTTCCACGATATACACCGCCCCCCTCCCGCCCCCTGCCCCAGGGATGCCCGGCTTTCCACCAGGTCTGTGCCTAAGCCTCAGAGGCTGTTCTATACAG
Seq C2 exon
GTGAGCGTCTCTTCCCCCTTGTCTACAACGTCCACGCCCACTTGGCCGGCAAGATCACGGGCATGCTGCTGGAGATTGACAACTCGGAGCTGCTGCTCATGCTGGAGTCCCCAGAGTCCCTCAACGCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000016849:ENSBTAT00000022412:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.719 A=NA C2=0.023
Domain overlap (PFAM):
C1:
PF0065813=PABP=PU(27.8=62.5)
A:
NA
C2:
PF0065813=PABP=FE(59.7=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:
GTCCAGGAGCCCGCTGTG
R:
AGGGACTCTGGGGACTCCA
Band lengths:
215-1648
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development