BtaINT0106821 @ bosTau6
Intron Retention
Gene
ENSBTAG00000017125 | PABPC4
Description
Bos taurus poly(A) binding protein, cytoplasmic 4 (inducible form) (PABPC4), mRNA. [Source:RefSeq mRNA;Acc:NM_001083724]
Coordinates
chr3:107094711-107096052:+
Coord C1 exon
chr3:107094711-107094841
Coord A exon
chr3:107094842-107095958
Coord C2 exon
chr3:107095959-107096052
Length
1117 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
CCGCCTCTCCTGGTTCCCAGGCA
3' ss Score
8.58
Exon sequences
Seq C1 exon
GTGTTCCCACAGCTGTGCAGAACTTAGCGCCTCGTGCTGCTGTTGCTGCTGCTGCTGCTCCTCGGGCTGTTGCACCTTACAAATATGCCTCCAGCATCCGCAGTCCTCACCCGGCCATCCAGCCCCTGCAG
Seq A exon
GTGAGGTCTACCAAACAGAACCCTAGAAGGGCTTCCCCTCTCTGCCCGTGATTTCAAAGCTGCCTTGCTTGGATTCCTTTACTAGGTATTAAATGCCTGCTCTGTGTCGGGGGGCTGTGTCCTGTGGGGGACTCTAGTGGGAGAGAAGGGGCTTGCAGGTGTTCTTCCTGATGAGAGTTGACTCAGCAATGCCCCGGAGGAGAAGCCTGCTTCCCGCTCTCCTCCTCACCATGTGCAGGGGCTCTCGCAGCTCTGAGCTTCCATTTCACTTTCACATCCAGCGGCTGAATTGATCCTTAGTTGCTCTGCAAGGTAATGGGGTGAACATCTTACAGATGAAAGGCTTGGCTTCAGAGGTATTAGGGTGAGTTGGAGGAATTGGACCCGGATCCCAGGGTTTCTGATCTGGAACTGCTGTCTCTCCAGCTGGGCCCCTCAGGGAGGTCAGACAGGGAGCTTGTGATAGAACTCTGCAGTTTGCTTGGGGGAGTGCTGCTGGGCCTTGTTTCCTCCTGCTCCATGCTGTAGGTGGGAAATTTCCCAGGAGGCCCTATGTGAACTTTGCCCACAAGGCCCTTCTTTTAAACGACTGTGACTGGTATTGACATTGCGAGTTGACGGTCCTCAAGCATTTGATATAGTAAACAGGTGGTGCAGTAAAGGAGGTACAGGATGCAGTTATAAGCATTTTGCTATTTCTGTCCTTTCACCCAGTTTCTACTGAAATTCACCCCTAAAGGAAAACTTTTAGCAGACAACTGCACATACCAGTGTTCACAGGACCTTGTTTATTATCAAGGCTTTGATGCCTTCGGTAAATTATGATCACTGGCCTTGAGTCAATTAAAATTACTTGGTAGATGACTGCCTAGCACTGTAGGTTTTTCGTAATCATTTCCCTTGCCTTCGAGTAGTGTGCCATTTTAATTGGTTGTTGGTTTTTTCCTCACACCACTCTCTTCCTCCCTCTCAGTCCGCCAAGACTGAAGTCAGTTCCCCGACAGCAAGGACAGCTGCGTCCATCTCCTCTTTCACTCAGTAGACTTGAGCGGTTGGGCTCATGACCGCTGTCACTGTCCTTTGCGTGTGTTAACCTGCCGCCTCTCCTGGTTCCCAG
Seq C2 exon
GCACCCCAGCCTGCGGTCCACGTGCAGGGGCAGGAGCCGCTGACCGCCTCCATGCTGGCTGCAGCACCCCCCCAGGAACAGAAGCAGATGCTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000017125:ENSBTAT00000022761:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.432 A=NA C2=0.875
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0065813=PABP=PU(27.8=62.5)
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:
GTGTTCCCACAGCTGTGCAG
R:
GCATCTGCTTCTGTTCCTGGG
Band lengths:
222-1339
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]