BtaINT0106792 @ bosTau6
Intron Retention
Gene
ENSBTAG00000046358 | PABPC1
Description
Bos taurus poly(A) binding protein, cytoplasmic 1 (PABPC1), mRNA. [Source:RefSeq mRNA;Acc:NM_174568]
Coordinates
chr14:65830113-65830891:+
Coord C1 exon
chr14:65830113-65830267
Coord A exon
chr14:65830268-65830806
Coord C2 exon
chr14:65830807-65830891
Length
539 bp
Sequences
Splice sites
5' ss Seq
CAGGTGTGG
5' ss Score
6.34
3' ss Seq
TTTTCCCATTTTCTTTCTAGCCC
3' ss Score
10.06
Exon sequences
Seq C1 exon
CTAACACATCAACACAAACGATGGGTCCACGTCCCGCAGCTGCTGCAGCTGCAGCTACTCCTGCTGTTCGCACCGTTCCACAGTACAAATACGCTGCGGGAGTTCGCAATCCTCAACAGCATCTGAATGCACAGCCGCAGGTCACCATGCAGCAG
Seq A exon
GTGTGGGTTTGATGGCTTCTTTATGATGACAGTCCTTGACTGCAAGGACTTTGAGGACAGCCATATGATGTGTGAGAGCTTAAGCTATCTAGAACATTTTGTTGAAGTCCCACTAATGGCTAATATGTAAAAATACGTGCTATACTCCAGGAACTAGAGCAGCGTTTTCCCTTCCTGAGTTGCTTATGTGGTTTGAGAGTTTTATTTGGCATAGTTGTAAGAAAGGGTGAAATAAAGTTTAGTTTGTGAGATTTGGCTTACTGTTTTTTGGTTTTTTTGACCCCTGGGACCAAAATTGTGGTTGATTATACTAGAAGTATGGTTCCAAAGACTACTCCAGATAAAGAAAATTCAACACCCCTGTGCTTATAATACTTGAGCACTTAGGTGTTAATAGCTGCCTTAGGCTGCATTTTCTGGTTCACTCAGCTTCTCCTGTTTGTTTAGATTATAGTCTTTATTCAGTTATTTTCCAGTGATGACTGTATTTGTGCTTGCCATTACTTCTGTACTTAGGAATTTTCCCATTTTCTTTCTAG
Seq C2 exon
CCCGCTGTTCATGTACAAGGTCAGGAGCCTCTGACTGCTTCCATGTTGGCATCTGCCCCTCCTCAAGAGCAGAAGCAAATGTTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000046358:ENSBTAT00000064237:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.846 A=NA C2=0.966
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0065813=PABP=PU(27.8=69.0)
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:
AACACATCAACACAAACGATGGG
R:
CCAACATTTGCTTCTGCTCTTGA
Band lengths:
238-777
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development