BtaINT0114590 @ bosTau6
Intron Retention
Gene
ENSBTAG00000001353 | PMPCA
Description
Bos taurus peptidase (mitochondrial processing) alpha (PMPCA), mRNA. [Source:RefSeq mRNA;Acc:NM_001076964]
Coordinates
chr11:103921287-103922029:+
Coord C1 exon
chr11:103921287-103921387
Coord A exon
chr11:103921388-103921765
Coord C2 exon
chr11:103921766-103922029
Length
378 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGG
5' ss Score
8.41
3' ss Seq
CCTCTCACTTGCGTGCCCAGGCG
3' ss Score
8.47
Exon sequences
Seq C1 exon
ACGAGGAAATTGAGATGGCGCGCATGGCTGTGCAGTTTGAGCTGGAGGACCTCAACATGCGGCCCGACCCGGAGCCGCTCCTCACCGAGATGGTTCACGAG
Seq A exon
GTGAGGCGGGCGCGGCGCCCCGGGGCCACCTCTGGAGACGCCTGGGATTTCTCAGGTGTCAGCAGTGCCCGCTGTAAACTCACCAGCCCTCAGAGCAGTGAGAGCTCTGGGACGTGCCCTTTATGTTTCGTACGAGCTCTCATTCCGGAGCGGCGGGCTTTACTATTTTTGTAAACGCACAAAGCTGCTCCACCAAGCAGTAGCTGAACCAAGCCGCTGGCGGCTTCCCGTCTGCTGGGGGTCGTCGCGGGCCAGCTCTCGGGGGGCTGAACCAAGCCGCTGGCGGCTTCCCGTCTGCTGGGGGTCGTCGCGGGCCAGCTCTCGGGGGCCTGGCCGCCTTCTCTGTGTCACGTGTGTTCCTCTCACTTGCGTGCCCAG
Seq C2 exon
GCGGCGTACAGGGAAAACACGGTGGGGCTCCACCGTTTCTGCCCCGCGGAGAACGTCGGAAAGATGGACCGGGACGTGCTGCACGCTTACCTGAGGAACTACTACACCCCTGACCGCATGGTGCTGGCCGGGGTAGGGGTGGAGCACGCACAGCTGGTCGAGTGCGCCCGGAAGTACCTCCTGGGGACCTGTCCCGCCTGGGGCACGGGGGCGGCCGTGCACGTGGACAGATCGGTGGCTCAGTACACTGGGGGCATCGTCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000001353:ENSBTAT00000001782:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.176 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0067515=Peptidase_M16=FE(21.9=100)
A:
NA
C2:
PF0067515=Peptidase_M16=PD(9.9=17.0),PF0519316=Peptidase_M16_C=PU(33.5=76.1)
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:
GAAATTGAGATGGCGCGCATG
R:
TGTACTGAGCCACCGATCTGT
Band lengths:
343-721
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development