BtaINT0106798 @ bosTau6
Intron Retention
Gene
ENSBTAG00000046358 | PABPC1
Description
Bos taurus poly(A) binding protein, cytoplasmic 1 (PABPC1), mRNA. [Source:RefSeq mRNA;Acc:NM_174568]
Coordinates
chr14:65823919-65825416:+
Coord C1 exon
chr14:65823919-65824058
Coord A exon
chr14:65824059-65825321
Coord C2 exon
chr14:65825322-65825416
Length
1263 bp
Sequences
Splice sites
5' ss Seq
TTGGTAATG
5' ss Score
4.83
3' ss Seq
ATCATTAAATTTTTTTTCAGGAC
3' ss Score
9.02
Exon sequences
Seq C1 exon
ATTTGTTGGAAGATTTAAGTCTCGTAAAGAACGAGAAGCAGAACTTGGAGCTAGGGCAAAAGAGTTCACCAATGTTTACATCAAGAATTTTGGAGAAGACATGGATGATGAGCGCCTTAAGGATCTCTTTGGCAAGTTTG
Seq A exon
GTAATGTGTCTGAATTAAATTTTTATATTCACATTGTTAATTTTGGATAATATTTTATACTAAAAATAAATGAGACTTATCATGGTACTTAAATTTTGTAGTTAATTTGGATTAAGCTACTGATAGTCCATTATACTAGCATATCAGTAAAATTCTATCCAGTTTAAAGGTCAATAGCCTTGCGTTAGCACAGTAAGTTGTGATTGTAATTGGAACAGACTTTAAAAGGTTTTGCCATGTTACGAAATTGTGCTGGATTTATGCACTAACAGATCCCATCTCAACAGAGGCATTGCATGTGACACAGCCAACTTAGGTTGGAATGTAGTCTTTAATTATGGGTTAGGAAAGCTGGCCAGCTTTAGGATATTTGGCCAGTCTCAGCATCATGTTTGAGCAATTCAAAATAATAACTTCAACGATCCAGATTTTCCAGTGAAGTGTAACCAGTCTCACTTTAGACAGTTGTGTAGCTGATCAGAAGATGAACCTGACATTGTACTCTTGCGGATGATTTGCTTGCCCCTTAACTTTGCTTCCCCTTCTGGTTAACTTAAACAGGTGTCCTGTTTTTTTAAGAGTATTTCAAATCATAAAGAATCAGGAAACATAATCCTTTATTATTGCCAAGCTGTCATGCCACATTGAACCCTCTAAACAGTCGTATCTGTGCCCATAAATCTTGCAGATTCTCTGTAATTAGATGTGATTTTTTTTTTTTAACCTTTTCCCCCACCTACCTAAAATAATACTCAGTTCAGTTAAGTCTATTTTATTGAGGGGTTAGTGGGGGAGAAGTGTGTCTTCAGAAACATGCCATCTCCAGGTACTTCTGTTTTGTCTTCCCCAAAGGTCAAACCCTTTGTTTCCTCTACTCCCTGTTGAAAATCAAGTGGGCCAAGGCTTAAGGAATTCTTAAGAAAATCAAGTTGTTTTAGAACAATGCATCTGTTTTGTACTAAATGCTAAGAATAAATTAACTCTGTCATTTACATTTGTCTGAAACATAGCGCCTTAAATGGAAGGAGGAATATTTCAGAGAAAGAGTTTACTTAGCTTCTTAGAAGAAATAAAGGGTCTTTGAAGAGAATGTTTAGTGCCCATGATAGGAGAGAGGGTAATTAGAGGAGGAATAAATTTCTGGAGGTTTGGGATTTTTTTTAATCCCCATTTTTATATTCTTTTCTGCACAGGTTTTTTGAAACTTAAAACATATAAACTTAAATGTATGGGATATATTTGAATCATTAAATTTTTTTTCAG
Seq C2 exon
GACCTGCCTTAAGTGTGAAAGTAATGACTGATGAGAGTGGAAAATCCAAAGGCTTTGGATTTGTAAGCTTTGAAAGGCATGAAGATGCACAAAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000046358:ENSBTAT00000064237:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=PD(1.4=2.1),PF0007617=RRM_1=PU(31.4=45.8)
A:
NA
C2:
PF0007617=RRM_1=FE(44.3=100)
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:
ATTTGTTGGAAGATTTAAGTCTCGT
R:
CATCTTCATGCCTTTCAAAGCT
Band lengths:
227-1490
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development