BtaINT0106804 @ bosTau6
Intron Retention
Gene
ENSBTAG00000016849 | PABPC1L
Description
poly(A) binding protein, cytoplasmic 1-like [Source:HGNC Symbol;Acc:HGNC:15797]
Coordinates
chr13:74043097-74046106:+
Coord C1 exon
chr13:74043097-74043289
Coord A exon
chr13:74043290-74045912
Coord C2 exon
chr13:74045913-74046106
Length
2623 bp
Sequences
Splice sites
5' ss Seq
ACGGTGAGC
5' ss Score
9.44
3' ss Seq
CTTTCTCTCCTCCTGTCCAGCGG
3' ss Score
9.46
Exon sequences
Seq C1 exon
ATGAACGCCAGCGGCCCGGGCTACCCGCTCGCCTCGCTCTACGTGGGCGATCTGCACCCGGACGTGACCGAGGCCATGCTCTACGAGAAGTTCTCGCCCGCTGGCCCCATCCTGTCCATCCGCGTGTGCCGCGACGTGGCCACGCGCCGCTCGTTGGGTTACGCCTACATCAACTTCCAGCAGCCCGCGGACG
Seq A exon
GTGAGCCCCCGAGGGAGAGGTGGAGCCGCGGGTGCGGGGGGTGGGGTGGTGGTGATGGACAGACAGACTGTATCCCAGCCACCAGCGCTCTTTCATCTCTGGCTACTCCCGCACCTTCCATTTTGCAGCCAGGAAAACTAAGATCCAGAGTTGCAGGAGAAGGGCCCTGAGATAGGAACTAGCAATTAGTGTGCCCGGAGATCAGCCCTGGGATTTCTTTGGAAGGAATGATGGTAAAGCTGAAACTCCAGTACTTTGGCCACCTCATGCGAAGAGTTGACTCACTGGAAAGGACTCTGATGCTGGGAGGGATTGGGGGCAGGAGGAGAGGGGGACGACAGAGGATGAGATGGCTGGATGGCATCAACTCGATGGACGTGAGTCTGGGTGAACTCCGGGAGTTGGTGATGGACAGGGAGGCCTGGCGTGCTGCGATTCATGGGGTCGCAAAGAGTGGGACACGACTGAGCAACTGAACTGAACTGACTGTTTCACTGGTGCTCCGTCTTCCGGAAGAGAGGTGATGCTGCTGAGTGAAAACAGCCAAGGGCTTTGGGGTCAGCCAGACCTGGGATTGGAAGGCCAGCAACGGTGCGATCTTGAGCAAATGAGTCATTCTGAGGTTCAGTTACCTGTCTGCAAAATGGGAGTGTCACCTGCCTTGTAGAGTGATTGGGAGAAAAGCAATGCACACCAGCCAGTGAGGAAGATGCCCCGGAAGGCACAGGTGATGGTGCGTGGGGCAGCTAGGAGTGCTCGGCCTCGGTCTGCGGCCTTTTCTGACAGCAGATCTCGAGGTCTGTCTGCATCAGGCACCTCCACTTTGGGGAACCCCAAAAAGCTGCCTCCCCTCTGGAGTCCACAGCCCATTTCTCAGAACTGATAGGATCGATCAGAGCTTGCCAGCTGGGTATGTCTTGACTTCTGTTCAGAGCCGAGAGGAGAAAAATTAAGAGCGCTGGGTTTTGTTGGAGCTCTGCCATGAGAGTGTGAGCTTGAGCAAGTCGTCACACTTGGCTCCTCTTTTTCTGTAAAATGGAACTAAGGCTTGTTCCCGAGGAGCATGGAGGGAATGGGGATTGTGTCTAGGAAGTAGTTCCAGTGTCATGTGGTACATTGTAAGCCCTCGGTAAGTGCAAATCTAAGAAAAATCCTGGTAACTATAGCATGTGTAAGGTAACTCTAGCAGGTGTGAGACTCTGGAGAAGTAACCAGAAGAGGCCTGTCCCAGCCAAGTCCACAAGGGGGCGCCTTTACTCTGAGGCTCCTGGGAGGCTGGGGAGGTTCCCGCCTCTGGGAGTTTGCTGGGGAGGTTTGGCTGGTTTCCCAGCAGGTGACTGAGTCGGATTCCAGGGAGATTTCCCCTCTGCTCTGCTTCACCCAGCCACTGCCTCTTGCTGTCTTCCGCCAAGTCCTGTACAACCTGATTTAATAGAATGGGAAATTGAGCTCCAGACAGGAGAAGGAGTTTACTCCTGGCTGTTTATGGCAGGACTAGATGGAAAACCCAGACTTCTCCAAACTTGTCCACTGAGTATTCCTCAGTTCCCCTCCATGCCTCTGAAACCTGAAGTGTCCCTGTAGCTGGGGACAACACGCCACCTGGCAGGACGATGGGCATATGCTGTTGTGCTTAGACATACTACTGTTTACCACATACCTATTTGAGCTAGGCACAAGGCGCTTTGCACAGGTTATTTAATTTTTAACACGAAAAAAAATGATTGATTTATTTATTTGGCTGCACCTGGTCTTTATTGCAACATGCGGGATCTCTTAGTTGCAGCATGCAAACTCTTAATTGCAGCATGTGGGATCTAGTTCCCTGACTAGGGGTGGAACTCGGGCCCCCTGCATTTGGGAACGTGGAGTCTTAGTCACTTGACCACCAGGGTAGTCCCACACCTTATTTAATTTTCAGTCTGTCTGACAAGCTGGAGGTGGGTGATATTCTCTCCCTTTGTTAGATGTAGAAAGTGTGTTAGTCAATCAGTTGTGTCCGATTCTTTATGACCCTGTGGGCTGTAGCCCACCGGGCTCTGTCCATGGAGTTCTCCAGGCAAGAATACTGGAGAGAGTTGCCATGCTCTTCTCCAGGGCATCTTTCCAACCCAGGGAATGAACCTGAGTCCCCTGTATTGCAGTGGATTCTTTACCCACTGAGCCACCAGGGAAGTCCTTGAGTAGTATAATCATCACCACTTCTTTCCAAGTGTAGAAATGGACTCAGAGATGTGATGTTCACTTTCCCGAAAGCCATCCTCTTTGGGATCAAATCTCAACTCTGCTGGCCAGCACCTCTGAGCTTCACTTTCCTCAAACTCCTGCCACCCTTGTCATAGGGACCCTTTTGATCATTTCCCCTTCTGAGCCTCAGTTTGTCTTTTTATAAAATGGGGGTAGAAACTCATGCTCATTTCACTATGATAAAAGAGTTGAAGGAGAGCCTACCTGGAAGCCACACACATGAATTCTATTTATTCTTCTTGAGCCTTCAAGCTCTTATCTCGAGTGAGACCCAGCCAGTGGCTCATTTATTGATCGGCTCAGCTCCCAATTAAGTTGTTGAGGGCTCAGGGAAAGAAAATGCCCTTAATTAGCTCCTTTCTCTCCTCCTGTCCAG
Seq C2 exon
CGGAGCGGGCACTGGACACCATGAACTTTGAGGTGATCAAAGGCCAGCCCATCCGCATCATGTGGTCCCAGCGAGACCCAGGACTTCGTAAGTCAGGTGTGGGCAACATCTTCATCAAGAACCTGGAGGACTCCATTGATAACAAGGCCTTGTACGACACCTTCTCCACCTTTGGGAACATCCTGTCTTGTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000016849:ENSBTAT00000022412:1
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
Rat
(rn6)
No conservation detected
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