BtaINT0106802 @ bosTau6
Intron Retention
Gene
ENSBTAG00000046358 | PABPC1
Description
Bos taurus poly(A) binding protein, cytoplasmic 1 (PABPC1), mRNA. [Source:RefSeq mRNA;Acc:NM_174568]
Coordinates
chr14:65828660-65829433:+
Coord C1 exon
chr14:65828660-65828932
Coord A exon
chr14:65828933-65829342
Coord C2 exon
chr14:65829343-65829433
Length
410 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGT
5' ss Score
10.28
3' ss Seq
CGTTTGCTTGCTTCCAACAGACT
3' ss Score
7.72
Exon sequences
Seq C1 exon
GTTATGATGGAGGGTGGTCGCAGCAAAGGTTTTGGTTTTGTATGTTTCTCCTCCCCAGAAGAAGCCACTAAAGCAGTTACGGAAATGAACGGTAGAATTGTGGCCACCAAGCCATTGTATGTAGCTTTAGCTCAGCGCAAAGAAGAGCGCCAGGCTCACCTTACTAACCAGTATATGCAGAGGATGGCAAGTGTAAGAGCTGTGCCCAACCCCGTAATCAACCCCTACCAGCCAGCACCTCCTTCAGGTTACTTCATGGCAGCTATCCCACAG
Seq A exon
GTAGGTTCTAGAAAAGGACAAAAACCTCATGAAGGTTTTCCTGTTAGGTCACCTTCCTTTAATGTTTTGTCATCCCCCCCCACCCCACCCCCCAAAAAAAGAGAATAAAGTCTTAAGATGAAAACATTGAGATGTGAATTATGATTGCATTTGAAAAATGCTTAAGAGTGTGCATGCTATGTACTAAGTCACTTCAGTCGTGTCTGACTTTGCGACCCTATGGACTGTTGTAGCCCCCCAGGCTCTTCTGTCCATGGGATTCTCCAGGCAAGAATATGGGAGTAGGTTGCTGTGCCCTCCTCCTGGGGATCTTTCCTGGAGTGTGAGGACCTGTTAACTATTTTGAACATGCATAATGTGTTGTATTATCTGCTTTTTCTATGACTGATACGTTTGCTTGCTTCCAACAG
Seq C2 exon
ACTCAGAACCGTGCTGCATACTATCCTCCTAGTCAAATTGCTCAACTAAGACCAAGTCCTCGCTGGACTGCTCAGGGTGCCAGACCTCATC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000046358:ENSBTAT00000064237:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.308 A=NA C2=0.742
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=PD(56.5=42.9)
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:
GTTATGATGGAGGGTGGTCGC
R:
CTGAGCAGTCCAGCGAGGA
Band lengths:
348-758
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development