BtaINT0106796 @ bosTau6
Intron Retention
Gene
ENSBTAG00000046358 | PABPC1
Description
Bos taurus poly(A) binding protein, cytoplasmic 1 (PABPC1), mRNA. [Source:RefSeq mRNA;Acc:NM_174568]
Coordinates
chr14:65819746-65821682:+
Coord C1 exon
chr14:65819746-65819939
Coord A exon
chr14:65819940-65821566
Coord C2 exon
chr14:65821567-65821682
Length
1627 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGC
5' ss Score
10.22
3' ss Seq
TGGTATACATTTTTCCCTAGGTG
3' ss Score
9.61
Exon sequences
Seq C1 exon
CGGAGCGTGCTTTGGACACCATGAATTTTGATGTGATAAAGGGCAAGCCAGTACGCATCATGTGGTCTCAGCGCGATCCATCACTTCGCAAAAGTGGAGTGGGCAACATATTCATTAAAAATTTGGATAAATCCATTGATAATAAAGCACTGTATGATACATTTTCTGCTTTTGGTAACATCCTTTCATGTAAG
Seq A exon
GTAAGCAAAAATGTGATAAGTAAACATAATTTACTGTTCATGGGGTTCTCAAGGCAAGAATGTTGAAGTGGTTTGCCATTCCCTTTTCCAGTGGACCATGATTTGTCAGAACTCTCCATCATGACCCATCTTGGGTGGCCCTGTGAGCTACAGCATGGCTCAGTTTCATTGAGTTAGACAAGGCTGTGGTCCATGTGATCAGATTGGTTAGTTTTCTGTTCTGTGATTGTGGTTTTCAGTCTGTCAGCCCTCTGATGGAGAAGGATAAGAGGCTTATGGAAGCTTCCTGATGGGAGAGACTGACTGAGGGGGAAACTGGGTCTTGTTCTGATGGGCAGGGCCATGCTCAGTAAATCTTAATCCAATTTTCTGTCATTGAGCAGGGCTGTGTTTCTTCTCTATTGTTTGACCTGAGGCCAAACTATGATGGAGGTAATGAAGATAAAGGGCAACCTCCTTCAAAAGGTCCCATGCACGCTCACACTCATGCACTGCTGGACTGCCCCCAACCCTCCAGCAGGCCACCACTGACCCACACCTCCACGGGATACTCCTGGACGCTCATGCGCAAGTCTGGGTCAGTCTCTTGTGGAGTCACTGCTCCTTTCTCCTGGTCCTGGTGTGCACAAGGTTTTGTGTGGGCCCTCTCAGAGTCTGTTTACCCAGTCCTGTGTAGGTTCTGCTGGCTCTGTGGTGGGGTTAATGGTGACCTCCTCCAAAATGGCTTATTGCACCCAGAGCCCCTGCCCCACAGCAGTCCACTGCTGACCCGTACTTCCGCAGGAGACACTCAAACACAGTTCTGGCTCAGTCTCTGGGTCCTGGTGCGCACAGTTTCGCCCTTCCTACCATCTTGCTGGGCTTCTCCTTTGCCCTTGGATGTGGGGTATCTTTTTGGTGGGATCTAACATTCTCCTGTTAACTCCTGTCAGAGCCTAAATAGGCCCCAAAGATGAAAGTTGGATAAGACAAGGTGCTTGCTCTTACTGAGCACACAGTCATCTTTAACTAGATTATCAGAAACCAAATTTGGAAAATAATTGGGAACGCTGGTGTAGGTCAGAGAACCCTATGCGAAATACTTGGTTCAAAACAACAAACTATCCATGGTGGAGTTTGTCTCGTAATAGAAGGTTATAAAAATGAAAATTAAGTAATAAAAAAATTTTTAAGTGATAATAGTAAAAATATATCTAGGAGTTTCTCTGGAGCTGTTGTGGGTAGTGTGAGCAGCTGAACTGAACACTTATTACAGTGTTGTAGCCGTGTGCTTAGTCGACTGCTCAGTCTTGTCTGACACTTTGCAGTCCTTCGGACTGTAGCCTGCCAGGCTTCTCTGTTCGTGGGGTTTTTCAGGCAAGAATAGTGGAGTGGGTTGCCAACTCTTTCTCCAGGAATCTTCCTAATATAAAGACCAAACCCCCATCTCCTGTACCTCTTGCATTGCAGGCACACTGAGCCATGGGGAAGCTACTTGTTTATTCCTTAAGATAGCAGCTGTGCTTTCTGTTAATAGATATCTTTATTTCCCAAATACTGAGGTTAGGTAGCTGACAAGTTATCTGAACATTGGAAAAATCCTAAATCAATAGTAAGTAATGAAAAATTGGTATACATTTTTCCCTAG
Seq C2 exon
GTGGTTTGTGATGAAAATGGTTCCAAGGGTTATGGGTTTGTGCATTTTGAGACACAAGAAGCAGCTGAAAGAGCTATTGAAAAAATGAATGGGATGCTTCTAAATGATCGCAAAGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000046358:ENSBTAT00000064237:2
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(25.4=27.7),PF0007617=RRM_1=PU(40.6=43.1)
A:
NA
C2:
PF0007617=RRM_1=FE(55.1=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:
CGGAGCGTGCTTTGGACAC
R:
ACTTTGCGATCATTTAGAAGCATCC
Band lengths:
310-1937
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development