BtaINT0106829 @ 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
chr3:107090554-107091316:+
Coord C1 exon
chr3:107090554-107090691
Coord A exon
chr3:107090692-107091220
Coord C2 exon
chr3:107091221-107091316
Length
529 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
CAGAGATCTTTCTGCTTCAGGGG
3' ss Score
5.57
Exon sequences
Seq C1 exon
GCTGTGGAAGAGATGAATGGAAAAGAAATCACTGGGAAGGTCATTTTCGTTGGCCGTGCACAAAAGAAAGTGGAGCGGCAGGCCGAGTTAAAGCGAAAATTTGAACAGCTGAAGCAGGAGAGGATTAGTCGCTATCAG
Seq A exon
GTGAGGTGGTCTCAGCCCAGCCTGCCAGCAAGGATGTACCTCAAAGTATTGGCAAAAGCACCCTTTGATTGGTAGGCTTTCTCTTTGGGGACCACGAGTTTGCTCTTCTGATTTCTCCCAAGATCATCAGGTTTAAAAGGATATACCTACCAGATATAGCAGCAATTCTAGGACAGGGACAAAGATTTAAATTATTTGTGTAGGGACTCTGTTCTGTGTACTTAAATGATAGCCATTTGTCTGGAATGGTGGTGAGGCGAGCCCTGCTGGGGCTGGTGGCGAGCCTGCGCAGCTGTGAGGAAGGCTGGGACTGCATTGATGGCCCCGTCGAGTCTTCAGGTGGCCCTTCCTCAGCTTAGACCCTGCATCAGGGTCCCCAGCAGAGTTTGGGAGGACGTGGAGCTGGGCGCACAGCTTCTGCCTCAGTGGCAGGTGCTTGCCTGAGAATTCGCATTTCTAACGAGTCTGGGGATCACATTTTGAGAACCAGAATTTCAGGGCATGTGTAACAGAGATCTTTCTGCTTCAG
Seq C2 exon
GGGGTGAATCTCTACATTAAGAACTTGGATGACACCATCGATGACGAGAAGTTAAGGAAAGAGTTTTCTCCTTTTGGGTCAATCACCAGTGCTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000017125:ENSBTAT00000022761:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.087 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=PD(21.4=32.6)
A:
NA
C2:
PF0007617=RRM_1=PU(40.6=87.5)
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:
GCTGTGGAAGAGATGAATGGA
R:
AGCACTGGTGATTGACCCAAA
Band lengths:
231-760
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]