RetrogeneDB ID: | retro_btau_1058 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 24:30060230..30060866(-) | ||
| Located in intron of: | ENSBTAG00000014082 | ||
Retrocopy information | Ensembl ID: | ENSBTAG00000034032 | |
| 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_1058
ATGGTCGCCCCACCGCAGCTGCGGGCTCTGCTCTTTGTGATCAATGCACTATTGTGCAAGCGCTGCTACCACGCAGCACT
GGCCATGCTTAAGGGATTCCAGAACGGGGCAGTCTATGGAGCCAAAATCCGGGCCCCTCACGCGCTGGTCATGACCTTTC
TTTTCCGGAGTGGCAGCCTCCGGGAGAAGCTGCTTGCCAACCTGCAGGCCACGTACACCCACTCCTGGAACCTGGCCAGG
TTTGTGTTCCTCTACAAGGGACTCTGCGCCCTGCAGTCCCACGTCCAGGGCGAGACCTACCAGGCACATTCATTCGTGTC
TGCCTTCATCGGGGGCTTGCTGGTGTTTGGAAACAACAGTAACGTCAACAGCCAGATCAGCATGTACCTGCTATCCCGCG
TCCTACTTGCCCTGTGCCACCTGGGCGTGGAGAAGGGCTTCATCCCTGAACCCAGGTTGGACCCGTTTCCATGGTTCACA
GGGCTGGTGTGGGGGCTGGTGCTGTGGCTCTTCGAGTGCCACCGGCCAACCCTGCAGCCCTCACTGCAGTCGTCCACGAC
CTACCTGTATGAGGACAGCAACGTGTGGCACGACCTCTCGGACTTCCTTATCTACAACAAGAGCCAACCCTCCAAG
ORF - retro_btau_1058 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 92.92 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MVAPPQLRALLFAINALLSKRRYHAALAMLKGFRNGAVYGAKIRAPHALVMTFLFRSGSLREKLRAILQA |
| MVAPPQLRALLF.INALL.KR.YHAALAMLKGF.NGAVYGAKIRAPHALVMTFLFRSGSLREKL.A.LQA | |
| Retrocopy | MVAPPQLRALLFVINALLCKRCYHAALAMLKGFQNGAVYGAKIRAPHALVMTFLFRSGSLREKLLANLQA |
| Parental | TYTHSWNLARFVFLYKGLCALQSHVQGKTYQAHSFVSAFIGGLLVFGNNNNINSQISMYLLSRVLFALCR |
| TYTHSWNLARFVFLYKGLCALQSHVQG.TYQAHSFVSAFIGGLLVFGNN.N.NSQISMYLLSRVL.ALC. | |
| Retrocopy | TYTHSWNLARFVFLYKGLCALQSHVQGETYQAHSFVSAFIGGLLVFGNNSNVNSQISMYLLSRVLLALCH |
| Parental | LGVEKGFIPEPRLDPFPWFSGLVWGLVLWLFEYHRPTLQPSLQSSMTYLYEDSNVWHDLSDFFIYNKSQP |
| LGVEKGFIPEPRLDPFPWF.GLVWGLVLWLFE.HRPTLQPSLQSS.TYLYEDSNVWHDLSDF.IYNKSQP | |
| Retrocopy | LGVEKGFIPEPRLDPFPWFTGLVWGLVLWLFECHRPTLQPSLQSSTTYLYEDSNVWHDLSDFLIYNKSQP |
| 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 .05 RPM | 0 .27 RPM |
| SRP017611_kidney | 0 .00 RPM | 0 .71 RPM |
| SRP017611_liver | 0 .00 RPM | 0 .53 RPM |
| SRP030211_testis | 0 .00 RPM | 0 .38 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_1058 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_1058 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_1058 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,
|