RetrogeneDB ID: | retro_btau_259 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 1:55872820..55873456(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSBTAG00000033360 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PXMP4 | ||
| Ensembl ID: | ENSBTAG00000038738 | ||
| Aliases: | None | ||
| Description: | Peroxisomal membrane protein 4 [Source:UniProtKB/Swiss-Prot;Acc:A5PJL1] |
Retrocopy-Parental alignment summary:
>retro_btau_259
ATGGTCGCCCCACCGCAGCTGCGGGCTCTGCTCTTTGCGATCAACGCACTATTGCGCAAGCGCCGCTACCACGCAGCACT
GGCCATGCTTAAGGGCTTCCGGAACGGGGCAGTCTATGGAGCCAAAATCCGGGCCCCTCACGCGCTGGTCATGACCTTTC
TTTTCCGGAGTGGCAGCCTCCGGGAGAAGCTGCGTGCCATCCTGCAGGCCACGTACACCCACTCCTGGAACCTAGCCAGG
TTTGTGTTCCTCTACAAGGGACTCTGTGCCCTGCAGTCCCACGTCCAGGGCAAGACCTACCAGGCACACTCATTCGTGTC
TGCCTTCATCGGGGGCTTGCTGGTGTTTGGAAACAACAATAACATCAACAGCCAGATCAGCATGTACCTGCTATCCCGCG
TCCTATTTGCCCTGTGCCGCCTGGGCGTGGAGAAGGGCTTCATCCCTGAACCCAGGTTGGACCCGTTTCCATGGTTCTCA
GGGCTGGTGTGGGGGCTGGTGCTGTGGCTCTTCGAGTACCACCGGCCAACCCTGCAGCCCTCGCTGCAGTCGTCCATGAC
CTACCTGTACGAGGACAGCAACGTGTGGCACGACCTCTCGGACTTCTTTATCTACAACAAGAGCCAACCCTCCAAG
ORF - retro_btau_259 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 99.53 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MVAPPQLRALLFAINALLSKRRYHAALAMLKGFRNGAVYGAKIRAPHALVMTFLFRSGSLREKLRAILQA |
| MVAPPQLRALLFAINALL.KRRYHAALAMLKGFRNGAVYGAKIRAPHALVMTFLFRSGSLREKLRAILQA | |
| Retrocopy | MVAPPQLRALLFAINALLRKRRYHAALAMLKGFRNGAVYGAKIRAPHALVMTFLFRSGSLREKLRAILQA |
| Parental | TYTHSWNLARFVFLYKGLCALQSHVQGKTYQAHSFVSAFIGGLLVFGNNNNINSQISMYLLSRVLFALCR |
| TYTHSWNLARFVFLYKGLCALQSHVQGKTYQAHSFVSAFIGGLLVFGNNNNINSQISMYLLSRVLFALCR | |
| Retrocopy | TYTHSWNLARFVFLYKGLCALQSHVQGKTYQAHSFVSAFIGGLLVFGNNNNINSQISMYLLSRVLFALCR |
| Parental | LGVEKGFIPEPRLDPFPWFSGLVWGLVLWLFEYHRPTLQPSLQSSMTYLYEDSNVWHDLSDFFIYNKSQP |
| LGVEKGFIPEPRLDPFPWFSGLVWGLVLWLFEYHRPTLQPSLQSSMTYLYEDSNVWHDLSDFFIYNKSQP | |
| Retrocopy | LGVEKGFIPEPRLDPFPWFSGLVWGLVLWLFEYHRPTLQPSLQSSMTYLYEDSNVWHDLSDFFIYNKSQP |
| Parental | SK |
| SK | |
| Retrocopy | SK |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)
Expression validation based on RNA-Seq data:
| Library | Retrocopy expression | Parental gene expression |
|---|---|---|
| ERP005899_liver | 0 .00 RPM | 0 .14 RPM |
| ERP005899_muscle | 0 .00 RPM | 2 .11 RPM |
| SRP017611_brain | 0 .00 RPM | 0 .27 RPM |
| SRP017611_kidney | 0 .00 RPM | 0 .71 RPM |
| SRP017611_liver | 0 .00 RPM | 0 .53 RPM |
| SRP030211_testis | 0 .03 RPM | 0 .38 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_259 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_259 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_259 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000038738 | 2 retrocopies |
retro_btau_1058, retro_btau_259 ,
|