BtaINT0106832 @ bosTau6
Intron Retention
Gene
ENSBTAG00000019942 | PABPC5
Description
poly(A) binding protein, cytoplasmic 5 [Source:HGNC Symbol;Acc:HGNC:13629]
Coordinates
chrX:42008984-42011006:+
Coord C1 exon
chrX:42008984-42009046
Coord A exon
chrX:42009047-42009595
Coord C2 exon
chrX:42009596-42011006
Length
549 bp
Sequences
Splice sites
5' ss Seq
TCGGTCCGT
5' ss Score
3.06
3' ss Seq
TCTGAACTTCCTTTTCTCAGCCT
3' ss Score
5.66
Exon sequences
Seq C1 exon
GCCAGTCAGTCCCTCCGGACCCGCCGCGAGTCTCAGGCTGCCGAAATCACCGCGCATCACTCG
Seq A exon
GTCCGTACCCAGTGGGCATCTTGGGTATCTGGGCGGTCTCCGGTCCCCGGCGCGTGTGTCTGTCTGTCTGTTTCTCTGCGCGATTCGCTGCTTGCAGCCTTCCTGCCTGGCCGCAGGGCACCAAGTGTCCAGTTTGCCCTTTCGCTGACGCTGAGTGTCTATAGCGCGGCCTTAGTGAGCTGCGAGCCCGCCTGAGACCGACCGGCCAGGCAGCCGGCGGAGGAATACACGTTCGGCCCCTGCCCTTGTTGCTATCATTTTAAACCCACGGGAGCTTGAGGCCTATTTTTATGCAGAAAATCGGTCGTGAGGCCTCTGTCGACAAGGCTAGATGTGGGAAGCCAGCCTGCTGCTTAGTGATTTCTTACTATTTATCGGGGGAAGGGACATTTCTTTCCTACTACTGGCTTTTGAAACTGATTTTAGATCTGAATGGGTGGAAATTCTAAGCCCCCTTAGGGAGAATAGATTCGTTATTGGGGTGCTTTTTTCTCTGATGCGTTTGTTCTGAGCCTGCTGACCAGCTGTTTCTGAACTTCCTTTTCTCAG
Seq C2 exon
CCTCAACAGTGATTCTGAGTCTGCTTTTAGCTTTCTTCGCCTTGGCTTTTTTCTGTTTGTGAACAGCTGTTTGGCCCATAGCTTAGAGAAAGCAGCCTTTTTTTCTCTCCCAAGAGAGCCTTCTCCTTGTGCTCAGAGAGATGGGGAGTGGGGAGCCTAATCCTGCTGGCAAGAAAAAGAAGTACCTCAAGGCTGCCCTGTATGTGGGTGACTTGGACCCAGATGTTACTGAGGACATGTTATATAAAAAGTTCAGGCCTGCTGGACCTCTGCGCTTCACTCGAATCTGCCGTGACCCGGTGACCCGCAGCCCCCTGGGCTATGGCTACGTTAACTTCCGCTTTCCTGCGGATGCTGAGTGGGCACTGAACACCATGAATTTTGATTTGATTAATGGCAAACCATTCCGTCTAATGTGGTCTCAGCCAGATGATCGCTTAAGAAAGTCTGGAATTGGAAATATATTCATCAAAAACCTGGACAAATCCATTGACAACAGGGCCCTTTTTTATCTGTTTTCAGCTTTTGGGAGCATTCTCTCCTGCAAAGTCGTATGCGATGACAATGGCTCTAAGGGTTATGCCTATGTGCACTTTGACAGCCTGGCCGCTGCCAATAGGGCCATCTGGCACATGAATGGAGTGCGGCTCAACAACCGCCAGGTGTATGTTGGCCGATTCAAATTTCCGGAAGAGAGGGCTGCTGAAGTTAGAACTAGGGATAAAGCGACTTTCACTAATGTTTTCGTTAAAAACTTTGGAGATGACATGGATGACGACAAACTGAAGGAACTTTTCAGCGAGTATGGGCCAACTGAAAGCGTTAAGGTAATAAGAGATTCCAGTGGGAAATCGAAAGGCTTTGGATTTGTGAGATATGAGACACATGAGGCTGCCCAAAAGGCTGTGTTAGATCTTCATGGAAAGTCCATCGATGGGAAAGTGCTCTATGTAGGGCGAGCACAGAAGAAAATTGAACGTCTTGCTGAGTTAAGGAGAAGATTTGAGCGGCTGAGATTAAAAGAAAAAAGTCGGCCTCCAGGGGTGCCTATCTATATTAAGAACCTGGACGAGACCATTGATGATGAAAAACTGAAGGAGGAATTTTCTTCCTTTGGGTCAATTAGTCGGGCCAAAGTGATGGTGGAGGTGGGGCAAGGCAAAGGGTTTGGTGTTATCTGCTTCTCCTCTTTTGAAGAGGCTACCAAAGCAGTAGATGAGATGAATGGTCGCATAGTGGGCTCCAAGCCTCTGCAAGTCACTCTGGGCCAGGCCAGGCGCAGGTGGTGAGGATAAGAATGCTCAATTTATTTCAGCCTTAAGCTGGTGCCTACTTAGTTTGGGCTACTTTGTGATAAGAGGTTATTTTATGTCAATTAACAGGTTTTTTTTAAGTGAATACTTTCTTTTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000019942:ENSBTAT00000026566:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=NA
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
PF0007617=RRM_1=WD(100=18.5),PF0007617=RRM_1=WD(100=18.0),PF0007617=RRM_1=WD(100=18.3),PF0007617=RRM_1=WD(100=18.0)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAAATCACCGCGCATCACTCG
R:
TAACGTAGCCATAGCCCAGGG
Band lengths:
354-903
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]