BtaINT0114582 @ bosTau6
Intron Retention
Gene
ENSBTAG00000001353 | PMPCA
Description
Bos taurus peptidase (mitochondrial processing) alpha (PMPCA), mRNA. [Source:RefSeq mRNA;Acc:NM_001076964]
Coordinates
chr11:103916755-103918087:+
Coord C1 exon
chr11:103916755-103916829
Coord A exon
chr11:103916830-103917884
Coord C2 exon
chr11:103917885-103918087
Length
1055 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGC
5' ss Score
8.7
3' ss Seq
CACCGCCTTCTCTGTTGCAGGTT
3' ss Score
11.9
Exon sequences
Seq C1 exon
CAAGATGGCGGCCATGGTGCTGGCGGCGACGCGGCTGCTGCGGGGCTCGGGCTCGTGGGGCCGCTCGCGACCGAG
Seq A exon
GTGAGCCGAGGGCGGGCCGGGGGTCGGCCGGGGGCCGGGGCAGCCCGAGCCCCCCTGGGTGCCCCGCCTCCGGCTTCCCCATGCCGTGGCGCGGCGGCCGGTGAGCGGGCTGGGGGTGCGGGCCCCTGGCCCCGTCCCCGAGGCGACGGTGGGGCTTCCTCGTCTGGCGCCCCGGGCTCCGGCCCCGAGCTTCATCCGTCTCTCCTCCCCCTCCCGCTTCTCCCGGGCGGTCGGGGGCTTGTCCGAGGTCACGTGTCATCTCCGCCTCGGGCCCCTTCCGGCCGCANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGAATGAAGAGCAGCCTCCAAGGAGGTGTTAAGCCAAGAGAGGTGGGAAATGAGAGAAGGGTTAGCCCTGTGAGCAGTGCTCGTGAAGAAGGCAGGGCAGGCCCAGCTGCGGGCGTGATGAGCCAGTGTGTTGAGAGTGTGAACAGCGGGCCAGTGGGCGCACCTGGTGCGGCGGGGCTCGACGGGTTAGGAGATGAGTTTGGAGAGTGAGTGGGGGGTCAGAGCATACAAAGCCTTTGGGACCTGGTGAAGAGGTGTGGCTTCCATTTAGACTCCAGGGGGGCTTTTGAAGGGCAGAGCTTGGTCAGGTGCTCTGTGAGCAGAAACTGACTTGACCCACACAGCCCCCACCCGTAAAGGGCTGTTCCTACTGTTTCATAGACACAGCACCAGCTTGCCTCAAGGGCCTGGGCCCAGGCAGAATTTGTTCCGTCAGTGACGCCCTTGGTCACGCCTCTGCCCTGTCTCTGGGATGGTGTAGAAATCTCTGCATGAGGAGATGCAGGCTGCACCTTGGTGGCCACCACAGTTTACGCTGTTCTCTCTCTCTCTCTCTCTCTCTGTTTTTTCCGGTCGTTCCAGGTGTCTTGCAGGATGTCAGTTCCCCAACCAGAGATTGAGTCTGGGCCCCGGCTGTGAAAGTGCCGAGTCCTGACCACTGGGCTGCCAGGGAAGGCCGCAGCGTCTCATTTTCCTCATGCCTGCACCGCCTTCTCTGTTGCAG
Seq C2 exon
GTTTGGAGACCCCGCATACAGACGGTTCAGCAGTGGTGGGGCCTACCCCAACATCCCCCTCTCTTCCCCCTTGCCGGGAGTACCCAAGCCTGTTTTTGCTACAGTTGACGGACAAGAAAAGTTTGAAACCAAAGTTACCACACTGGACAATGGACTCCGTGTGGCATCCCAGAATAAGTTTGGACAGTTCTGTACAGTCGGGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000001353:ENSBTAT00000001782:1
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=0.014
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0067515=Peptidase_M16=PU(9.9=21.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAAGATGGCGGCCATGGTG
R:
TCCCGACTGTACAGAACTGT
Band lengths:
278-1333
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development