BtaINT0106795 @ bosTau6
Intron Retention
Gene
ENSBTAG00000046358 | PABPC1
Description
Bos taurus poly(A) binding protein, cytoplasmic 1 (PABPC1), mRNA. [Source:RefSeq mRNA;Acc:NM_174568]
Coordinates
chr14:65832127-65833756:+
Coord C1 exon
chr14:65832127-65832220
Coord A exon
chr14:65832221-65833310
Coord C2 exon
chr14:65833311-65833756
Length
1090 bp
Sequences
Splice sites
5' ss Seq
AAAGTGAGC
5' ss Score
5.89
3' ss Seq
TTTTTCCCCCACATTTACAGATG
3' ss Score
9.53
Exon sequences
Seq C1 exon
GTTGATGAAGCTGTAGCTGTACTCCAAGCCCACCAAGCAAAAGAGGCTGCCCAGAAAGCAGTTAACAGTGCCACTGGGGTTCCGACTGTTTAAA
Seq A exon
GTGAGCCTGCCTCCTGTTTCTTATTCTCACAGTTTGAGCGTGTATTGAAACATAGCAAAAACTCATTTTATCACTAATCCAAATGCATTGCCAGTTTTTCAAAGAGAAGTAAAGATACAGAGGAATTAACTACATATTACCCTGGTATAGACTTGAATTTTTGAGATCAAGACCCCTTCAGACGTTTTGCGTAGTAATTTGTGTTAAATAGCTGTAACATGGATTGGCCCTGTGTAGATCGCTGAAGGACTTTCATAGCTTAATACATTTTCTTGGGTGGCAGTTGTTTTTTGGCCTTTAATACTGCCTTTCATTACCCCCAAGAAATAGGGTGATGTAGCTTTGTAGCCAGAGCCAGGCGTGTGTACAAAGCTTTCCTATAAAATAGGAAATAGCTGGGGCTGTGCGGGGTGTGTTCCGTGTTGAAGCTCCTCTGCCCCGCTGTCACCCTGTGAGAGCGGCCGAGCAGCTTGTGAACCAGCAGGGGTGGCTGTGGTTCATAGAGCTTTACAGAGACAGGCTCTCGGCAGGCTGAACCTGGCTGAGGGCTTTCACACCCACAAGTGCCAGTGTTGGTCCTCTTACTTTTGTTTTTAGTAAAATACTTGACATAACAACATTGTGTAAATTTAAGGTGTGTAACGTGTAAATTGGATACATTTGTATATTGTAAGGAGAAGGCAATGGTACCCCACTCCAGTACTTTTGCCTGGAAAATCCCATGGACGGAGGAGCCTGGTAGGCTGCAGTCCATGGGGTCGAGAAGAGTCGGACATGATTGAGCGACTTCACTTTCACTTTTCACTTTCATGCTTTGGAGAAGGCAATGGCAACCCACTCCAGTGTTCTTGCCTGGAGAATCCCAGGGACGGCAGAGCCTGGTGGGCTGCCGTCTATGGGTCGCACAGAGTTGGACACGACTGAAGCGACTTAGCAGCAGCAGCATATATTGTAAAATACGACTATCATTATAGCTATAATTAGCACTTCTGTCACTTAGGTAAAGGTCCTTTCTTTTTAGTGGTTGGAATCATTATGTTCTGTGTCTTAAATTTGATGATCATAATCTCTTTTTCCCCCACATTTACAG
Seq C2 exon
ATGATCAGGGACCATGAAAAGAAACTCGTGCTTCACCGAAGAAAAATACCTAAACATCGAAAAACTTAAATACTATGGAAAAAAAAACATTGCAAAATAGAAAATAAATAAAAAAAGGAAAGGAAACTTTGAACCTTATGTACCGAGCAAATGCCAGGTCTAGCAAACATAATGCTAGTCCTAGATTACTTATTGATTTAAAAACAACAAAAAACACAAAAAAATAGTAAAATATAAAAACAAATTAATGTTTTATAGACCGTGGGAAAAAGAATTTTCAGCAAAGTACAAAAATTTAAAGCATTCCTTTCTTTAATTTTGTAATTCTTTACTGTGGAATAGCTCAGAATGTCACTTCTGTTTTAAATAACAGAATTGATAACTGAGCAAGGAAACGTAATTTGGATTATAAAATTCTTGCTTTAATAAAAATTCCTTAAACAGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000046358:ENSBTAT00000064237:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
3' UTR
No structure available
Features
Disorder rate (Iupred):
C1=0.667 A=NA C2=NA
Domain overlap (PFAM):
C1:
PF0065813=PABP=PD(9.7=22.6)
A:
NA
C2:
NA
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAGCCCACCAAGCAAAAGAGG
R:
GCTGAAAATTCTTTTTCCCACGGT
Band lengths:
351-1441
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development