BtaINT0106816 @ bosTau6
Intron Retention
Gene
ENSBTAG00000016849 | PABPC1L
Description
poly(A) binding protein, cytoplasmic 1-like [Source:HGNC Symbol;Acc:HGNC:15797]
Coordinates
chr13:74060421-74061810:+
Coord C1 exon
chr13:74060421-74060687
Coord A exon
chr13:74060688-74061725
Coord C2 exon
chr13:74061726-74061810
Length
1038 bp
Sequences
Splice sites
5' ss Seq
CAGGTGACT
5' ss Score
6.6
3' ss Seq
GGTCTTTCTCTCCTACACAGCCT
3' ss Score
7.2
Exon sequences
Seq C1 exon
GTGATGACAGAGGGTGGCCACAGCAAAGGGTTTGGCTTTGTGTGTTTTTCCTCTCCAGAAGAGGCGACCAAGGCCGTGACAGAGATGAACGGGCGCATCGTGGGCACCAAGCCACTGTACGTGGCGCTGGCCCAGCGCAAGGAAGAGCGGAAGGCCATCCTGACCAACCAGTACATGCAGCGCCTCTCCACCATGCGGGCCCTGGGTGGCCCCATCCTGGGCTCCTTCCAGCAGCCTGCCAGCTACTTCCTGCCCGCTGTGCCCCAG
Seq A exon
GTGACTGCCTGCCCACCCCCCTTCCGGGACGGCCAGGGAGAGCAGGCAGATCCCAGATTTGCAGGCAGAGAGGGATTCCCAGGGTGCTTCTGCTGGAAACTCACTCAGCAGGTGGCCGTGGTCACCCCATCTCTGAAAGGGGTAATAGTGTGTCCAACAGTGCTTCCTGATCTAGGAGAGATTTGTGAATATAGTGCAGAGAAAGACACTCTGTGGTCAAATACTGGGTTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCAACCCAATACATTGGGAAAAGATTGCATTAAGCCAGACAAGCCTAGATTTCTTTACCGTGTACCTTCTTCTACCCTACTATGCCAGCAGGCACCGTGACTTTCCCAAACTGGCAGGATTTACAGATTCTCCCAACTGAGGTGGTCATTTTTGAGGGCTGTCTGCTAACATCTCTCCTGATATCCTGAGGGGTCTTGTTTGGGGAAGGAGCTTGTGTAACCTGGAGGGGTGGGAAGATGTCTGTAGGAAGATGAATGGCTCAGAGAATGGGAACATTCCTTCCCCTTTGTGGTTACTTAAGCTGGCATGAGGGACAGTGGGATGTGTCACCATTTTATCCAGGTCACTGGGCTAGTACCACAGATCAGCAGAGCAAGGACTGAGCCTGAGATCTTGCCCTGAAGGGCTCAGGGCTAACGGACCTCCTGAGATGGGAAGCAGGAGCCTTCACCCCAACTTTCTGGGTATTTGCTGACCGGTCCCCTGAAAGGCAGACTGGCATTCCTGCAGTGGTGTCCTTGAGGGATGCAGTTGCTCACCTCTCCCCCTGCGCCCCCCGCTGCTGCCACCCCCCTTCACTCTAGGTCTTTCTCTCCTACACAG
Seq C2 exon
CCTCCAGCTCAGGCTCCCTACTATGGCTCTGGCCCACCCATCCAGCCTGCCCCCAGGTGGACGGCCCAGCCACCCAGACCGTCAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000016849:ENSBTAT00000022412:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.090 A=NA C2=0.862
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=PD(56.5=43.8)
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:
GATGACAGAGGGTGGCCACAG
R:
ATGACGGTCTGGGTGGCTG
Band lengths:
350-1388
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development