BtaINT0114586 @ bosTau6
Intron Retention
Gene
ENSBTAG00000001353 | PMPCA
Description
Bos taurus peptidase (mitochondrial processing) alpha (PMPCA), mRNA. [Source:RefSeq mRNA;Acc:NM_001076964]
Coordinates
chr11:103917885-103918593:+
Coord C1 exon
chr11:103917885-103918087
Coord A exon
chr11:103918088-103918513
Coord C2 exon
chr11:103918514-103918593
Length
426 bp
Sequences
Splice sites
5' ss Seq
GGAGTGAGT
5' ss Score
6.05
3' ss Seq
AATTTTCTTTTTATTACCAGTTC
3' ss Score
6.91
Exon sequences
Seq C1 exon
GTTTGGAGACCCCGCATACAGACGGTTCAGCAGTGGTGGGGCCTACCCCAACATCCCCCTCTCTTCCCCCTTGCCGGGAGTACCCAAGCCTGTTTTTGCTACAGTTGACGGACAAGAAAAGTTTGAAACCAAAGTTACCACACTGGACAATGGACTCCGTGTGGCATCCCAGAATAAGTTTGGACAGTTCTGTACAGTCGGGA
Seq A exon
GTGAGTACTGTTGGTGGTGTTGGGGGTGGTCCTGTTTGTTGCAAAACGCACACACCTCAGTCGACTGTGAGTTGTAATTAGGGCATAGTTAATAAACTGTGTCCTGAGTGAAAAAGCACATTATAGAATCTGAAGGTTTAGCAGCTGCAGAATGAACAGTAGCTGTCTCGGTGGTGGGTTTGTTTTCCCTCTTTCTACCTTTCTGTTACTCTAAAAATTTTCTACGGCGAGCATAAAGTGAAGAATCCTGTAAATACTGACGTGTGTGTACCCGTGAAGTGCTCAGAATTGAGACAGTGGACATGCTCATCACTCTCACGTGTTTAAATTTGGCTGTTTAGTTGTATTCACTCTTTTAAAAGGTTTGTCTTAAGTGTTTCCTGTTGAACATTTGGTTTAATCTGTCAATTTTCTTTTTATTACCAG
Seq C2 exon
TTCTTATTAACTCTGGATCAAGATACGAAGCGAAATATCTTAGTGGAATTGCTCACTTTTTGGAAAAATTGGCATTTTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000001353:ENSBTAT00000001782:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.014 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0067515=Peptidase_M16=PU(9.9=21.7)
A:
NA
C2:
PF0067515=Peptidase_M16=FE(17.2=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:
GTTTGGAGACCCCGCATACAG
R:
CGAAAATGCCAATTTTTCCAAAAAGT
Band lengths:
283-709
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development