BtaINT0106790 @ bosTau6
Intron Retention
Gene
ENSBTAG00000046358 | PABPC1
Description
Bos taurus poly(A) binding protein, cytoplasmic 1 (PABPC1), mRNA. [Source:RefSeq mRNA;Acc:NM_174568]
Coordinates
chr14:65816006-65819939:+
Coord C1 exon
chr14:65816006-65816689
Coord A exon
chr14:65816690-65819745
Coord C2 exon
chr14:65819746-65819939
Length
3056 bp
Sequences
Splice sites
5' ss Seq
ACGGTGAGA
5' ss Score
8.94
3' ss Seq
GAAAATGTCCTTTCTTGCAGCGG
3' ss Score
9.07
Exon sequences
Seq C1 exon
AGTGTGTGCTCCGGGCTCGGAACACACATTTATTATTAAAAAAATCCAAAAAAAATCTAAAAAAATCTTTTAAAAAACCCAAAAAAAAAATTTACAAAAAAATCCGCGTCTCCCCCGCCGGAGACTTTTATTTTTTTTTTCCTTCCTCTTTTATAAAATAACCCGGTGAAGCAGCCGAGACCGACCCGCCCGCCCGCGGCCCCGCAGCAGCTCCAAGAAGGAACCAAGAGACCGAGGCCTTCTCCCGCTGCCCGGACCCGAGACCGCCACCCTCGCTCCCCAGCCGGCAGCCAACAGCCAAGCCTCCAGCGGCAGCGGATCGACCCGGTTCTGCGGCCGTTGAGTAGTTCCCGATTCCGGTTGATTTTTGTCCCTCTGCGCTTGCCCCCGCTCCCCTCCCCCCGGCTCCGGCCCCCCGGCCCCGGCACTCGCTCCCCTTTTCTGACGGGAAAGGTCGCGCGGCCTGTGGCCCTGCAGGCAGCCGTGCCGAGATGAACCCCAGCGCCCCCAGCTACCCCATGGCCTCGCTCTACGTGGGAGACCTACACCCCGACGTGACCGAGGCGATGCTCTATGAGAAGTTCAGCCCGGCCGGGCCCATCCTCTCCATCCGGGTCTGCAGGGACATGATCACCCGCCGCTCCTTGGGCTACGCGTATGTGAACTTCCAGCAGCCGGCGGACG
Seq A exon
GTGAGAGCCGGGCCCGGCGGGCGGGCGGGCGGGCGGGCGGCCATGAGGCTCAGGCGGCGGCGGGCGGGCTAGGCCGGCGGGCCCGGGGGGGAGGGGGCGGGAGGGCATGTCACCCCACCCGAGGCCAGAGGGCCGAGGCTGGGGCTTCAGGACCCCGGATCCCCGCGCCGGCCGGGGCCCGCGCCGCCGGCAGCCGCACGCCCCTTGCACGCCGGGGCACTTCCTTCTCCGCGACCATTTTCTCGGCCTCAGCAGCGCTCAAACTTTAGGGTGATGACGCGCCCGGACGGTGGGTGAGGTTGGGTTCTAACACCACGCGGCGCCCCCCCCCCTCCCCCCCCGTTAGCGGCGAGATCCTGGGGGGTGTCGAGAGCCGAGACCCTTCTCCGGTAGTCGGTGGAGGCGCTCCCACCACCCCCAGGCTGCTGCCGGCGCCCCAGGACAGGGAGGAAGTGCATTTCGTTGCTCGAAAAATACCACGTGTTGAACCCGGTAACCTCCCAGGCCCTAGGCCTCTATCCTGCCGCGGGGCCAGTCGCCTGGGAGAGTCGCGGGGACTTTGAATAAAGTTAATCTGGTGCTCTGGTGGTCGTCCTCAGGTTTCTGCTACCATTCTCACTAACGTGTGAGTGACTGACGGCTCCAAAAGTGTAAATTACCACCGAGACGTTGCGTTGGGGGTTCAGACAGTTCTTGTAACAGCAAGTTAGGAGAGAAGGGATGTAGAAGATGACCCATCGTTTTCTCAGGCAATTTAGTTAGTTTTGATTTTTTAAATCTAGTAGTTTCGTAGTACTGGTAATTCGGGTTTTTTTTCTTTTTTCTTTTACCTCCTGAAATCGTCTCTGGTTTTGAAGGATTTTACTTAAAAATGTCATCCCCAATTTTGACTGTAAAATGTTGCTTGTGAGTGTAGTGTGTACTAGACCATTATACTTACGAGGTATTCTAGTGGTGATTTCCTTATAAAAGTGGTCCAGATTGTTCATACATCATGGGGAATGATTGACTGAAAAGTAAGGGATTAATTAGTTTGAATGTATGAGAAAAAAGATGGAATTAACCTTATATTTTTAAACAGTTCACAGAAATTCGAATATTTGGCAAATAGGTATGTGGCCTGATGAGTTGCCGGGATTTTTCTTTATAGCTGAAATCAATTGACTTGAAAAAGTCATTTTCACTTAATTTTATGATCCATTTTTGCCCTTTTTTCCCTTGGCTACTTGAATATATGTCAAGTATTATAAAATATAAGGAATTAATTTTTGTAGGAAAGGCCTGGAAGGTGGAATTTAAAACTTTTATCTCGTTAAGGAATTATTTTGTGGTCAGTTTTTCACTAGGTAAAGTGAATACTGAGATTTGGGGTAGACAGGCTGTTGAGCCACACCAAGTTGTAAAACTGCACTGCAGGTTTTCTGCCCTTTGCTCTGCAGGCAGTAGTTCCAAATGCCTCTCTGTAAGGATTCTTCCCAACTCTGATCAAGTTTATCACTAAATGGAAGATCAGGGAAGGTAATTTGGGTGCAGATAATCACAAACTGAAGGGTTGATAGAGAAAACTTGAACGAACAAATTCTAGAAATGTGAACTTTTGAAACTGACTGTTAACATAGTTTCTAAACTTAACAGTTTTAAATCAGAAAAAAAATTTAATTTCTTAGGATTTGAAAAGTTGAACTTCAGGTTACCATGGTTACAGTACACTCACTGTATTATTCTCTTTACCAGTAGACTTGTACTGTTACTGCTGAAAAGAAGGTAGCATTTTTCCATCTTCAGTTTATTTTATTCCTGTATGTATACAAATTATTCTCTTTCCAAATAAGTAAGTGATTTTCCTTCTACTCCCCTCTTATTTTGCAACATCGGTGTACTTGTAGAATAGCTGCTGAAAGTGATCAGTTTCCAATTTAACAGGAAAATGTGACTCATTCAAAAGAAGCTCAAGCAAAGTCAGCTAAAAAACTAGGGGAGCTGAGTAGGTGTGGCCAGTTGATAAATGAGCTGACAGCTGATTGTCACTATCTTCTAGAAACTGAAATTTTCATGTATAGAAAGAAGTGGCCGGAAAATTTGTTTTCTCACTTTACAGTTAACACTAGCATGGCATTTGTGAAAATTGATGTTTCAGAACTTCAAATGGATTGTGTGTGTCCCTTGTTTAGGAACTAGTCTTTTCTACTTAAGAGGATATATTTTTCCATTTAGAGTCCAAACTTCTTTAATAAGTGTTTCTTTAATGGTACAGGTGCACATAATTTGATCCTTCATAGACTCTGAACTCAGATTTTGAAGTTTTCTAGCACTATCCAGAAGTAACTAATCAGTTACTAAGTAAATGATCTAAGATAAAACTGGTTTTATATGTATTAATAGTGAGTTGGACTATTGTAAACCAGGTTATTTAAAAAATTTTTGTTAATAGCTAAATATGCTCAACTTCACATTAGTTTTTGAAGGCATGACTCAAATGATTCTGAACGGATAAAACCTTTCATTTTTTTTAACATGGTAGCAGGAAGTTGTGCCGTGAGTCACTGAAATCCCCCCAATACGTCAGGAACTTTTTTTTAGAAGATGGGCTAGTTTTTGTGTAATACTGACAGGAATAAGCAATAAAACATTTTTAACAAGTAGCAGGGAATAAGTTAAAATGCTTGAAAATCCGTAAACTGCTCTGCTTGTGGATAACCTATAGTTGCTTTTGGTGTCTTGTTATATTGTTTATCAAGCAGATTGTGAAGGGGAAATCTGTTTTTATAGTTAACTAGGAACAAAAAAGCGCTTTTAAATTTCATGGCAAAGGAAGAGATTGCTTCAGAAATATATTAGTTCTAAACAATATGTCATCTGTTAACGTGGGAAATTTGGGATTTCTTGATACTTGTCTTTGTGTTGTATGATATAAATCTAGACTGACAGGTATAAGGTCCAGCCATCTTCGGCTTAAAGAGGTAGAGGGGCTCAATTATTCTCTCCACAATAGATTATATTAAGTAGACTGTAAAAGTTTTGAATAATATTTACTTTGAAAATGTCCTTTCTTGCAG
Seq C2 exon
CGGAGCGTGCTTTGGACACCATGAATTTTGATGTGATAAAGGGCAAGCCAGTACGCATCATGTGGTCTCAGCGCGATCCATCACTTCGCAAAAGTGGAGTGGGCAACATATTCATTAAAAATTTGGATAAATCCATTGATAATAAAGCACTGTATGATACATTTTCTGCTTTTGGTAACATCCTTTCATGTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000046358:ENSBTAT00000064237:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=PU(73.2=80.0)
A:
NA
C2:
PF0007617=RRM_1=PD(25.4=27.7),PF0007617=RRM_1=PU(40.6=43.1)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development