BtaINT0116360 @ bosTau6
Intron Retention
Gene
ENSBTAG00000002178 | PPL
Description
periplakin [Source:HGNC Symbol;Acc:HGNC:9273]
Coordinates
chr25:3978853-3980330:-
Coord C1 exon
chr25:3980235-3980330
Coord A exon
chr25:3978976-3980234
Coord C2 exon
chr25:3978853-3978975
Length
1259 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCCT
5' ss Score
5.4
3' ss Seq
GGCCCTCTGGTCTCCCCTAGTTC
3' ss Score
8.19
Exon sequences
Seq C1 exon
GCTCACATGGAGGCTGTCCACGCAGATTGGAAGGAATACCTGAACCTGCTCATCTGCGAGGAGAGCCACCTGAAGTACATGGAAGACTACCACCAG
Seq A exon
GTGCCTGCCAGCCGGGCCCCATGGGGGGAGCACCCAGCGCCCACTTGGCTCCCTTGTGGGCTCAGCACCGCTTCCTTGGGAGCCTTTCAGAGCTGCCTTCCCACGCCTCCCGATGTCTGTGGTTCTCATGGTAGACATGCATGTGCCCTAAGATTTCCAGGCCCTTGTCTGCCTCCCCTGGGGGCTGGGACTGGAGAGTCTTAACTCACCAAGATGGCACAGGTGCAGGAATAGGTGTGTGGGGTTTTCGTTTTGGGATATGTATTGTATGAAGTTTGCCATTTTAGGCATTCTTAAGTGCACAACCCAATGCAGTGATTATATTCACAATGTTGTGCAACCATCACCACTGTCTTTCCAAAACGTGTTCACCACCCCAAGTAGAACTTCTGTACCTAATAAGCAGTCACCTCCCCCATTCCAACCCCTGATAACCACCCCTCTACTTTCTGTCTCTTTGGATTTGCCCATTTTAGATATTTCATAGAAGTGGACTCACATGATCTGTGGCCTTTTGTGTTTGGTTCTTTCACTGAACAAAACGTTTTCAAGGTTCATCATGAACCGGAACTTCATTCCTTTTCACGGCTGAATAATATTCCATCGATTCCATTGTATGCGTGGACCACGTTGTGTTTCTCCATTCACAATGTTGATGGATACTACAGTATTTCCACTGGAATGTGTTTTTAATAAGACAGCTGCACGTGATTCTTGTGAGCAGGCAGTTTGGGGACATTGGAACTCAGATGGCACTGACATAACTAACTCGGCGTCATAGTGTCTCAGTCCTGCCGGGCTGTGGACTTCCCAGGGATCCCAAAATCATGTTCAGCTGCAGCCCAGGGACAGCTGTCAGTGAATGATTCCAGAGCTGATAGGCTGAAAAACGGGCAAGAGAGTTTCCCAGAACCAAGTGGGGAGGCTTGCCTTCCATGTACTGAGGCTTAGAATAAGTCAGGGTGTTCCCAGCATAAAGACAGGAGTGGAATAGAGGAGAACCCTAAGGTTTCTGGTGTATGGACATGAAACCAGCTTGTCATAGAGGTGGCATTGCATGGATTGCTGAGAAGGGACCCAGTCTCTCCCTGTGAAGCCCCCCAGGAAGGTGGGCTGGGGAGGGCTGGGGGCGTCCCTGTGATTCAGGGTGAGTGGGAGGCCCAGCCCCACCTGGGAGTGGGCTTCAAGTCACAGCCAGGATGAGCCTCAGGCATCCTGGTGGACTCCCACCCATGATGGGGCCCTCTGGTCTCCCCTAG
Seq C2 exon
TTCCACAAAGACATGAAGGATGCCCAGGAGCTGCTTCGCAAGGTGGACTCAGACCTGAACCAGAAATACAGCCCTGACTTCAAGGACCGATACCAGATTGAGCTGCTGCTGCGGGAGCTGGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000002178:ENSBTAT00000002822:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.031 A=NA C2=0.049
Domain overlap (PFAM):
C1:
PF084565=Vmethyltransf_C=PD(8.1=40.6),PF0043516=Spectrin=PD(22.1=71.9),PF123293=TMF_DNA_bd=PD(2.8=3.1)
A:
NA
C2:
PF0043516=Spectrin=FE(50.6=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:
GCTCACATGGAGGCTGTC
R:
GCAGCTCAATCTGGTATCGGT
Band lengths:
202-1461
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]