RetrogeneDB ID: | retro_ptro_657 | ||
Retrocopy location | Organism: | Chimpanzee (Pan troglodytes) | |
| Coordinates: | 12:6637378..6638812(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PKP2 | ||
| Ensembl ID: | ENSPTRG00000004820 | ||
| Aliases: | None | ||
| Description: | plakophilin 2 [Source:HGNC Symbol;Acc:9024] |
Retrocopy-Parental alignment summary:
>retro_ptro_657
ATGCTCGATGCAGACCAGATGCCGCCGTCCAGGATTTCTGCCGCAGCCACTTTCATACAGCACGAGTGCTTCCAGAAATC
TGAAGCTGGGAAGAGGGTTAACCAGTTTTGTGGCATCCCCAAGCTTCTGCAGCTCCTAAAAGTTCAGAATGAAGATGTTC
AGCGAGCTGTGTGGGGGGCCTTGAGAAACTTACTATTTGAAGACAATGACAACAAATTGGAGGTGGCTGAACTAAATGGG
GTAACTCGGCTGCTCCAGGTGCTGAAGCAAACCAGAGTCTTGGAGACTAAAAAACAACTAACAGGTTTGCTGTGGAATTT
GTCATCTAATGACAAACTCAAGAATCTCATGATAACAGAAGCATTGCTTATGCTGACCGAGAATATAATCATCTCCTTTT
CTGGATGGCCTGAAGGAGACTACCCAAAAGCGAATGGTTTGCTCGATTTTGACACAGTCTGCAACGCCACTGGATGTCTA
AGAAACATGAGTGCTGCTGGCCCTGATGGGAGAAAAGCAATGAGAAGACGTGACCGACTCATTGACTCAGTGGTCCATTA
TGTCAGAGGAACCATTGCGGATTACCAGCCAGATGACAAGGCCATGGAGAATTGTGTGCACATTCTTCATAACCTCTCCT
ACCAGCTGGAGGTAGAGCTCCCAGAGAAATATTCCCAGAATATCTATATTCAAAACCCAAATGTCCAGACTAACAACAAA
AGTATTGGATGTTTTGGCAGTCGAAGCAGGAAACTAAAACAGCAATACCAGGACATGCCGATGCCAGAGGAAAAGAGCAA
CCCCAAGGGCGTGGAGTGGCTGTGACACTCCATCGTGATAAGGATGTATCTGTCCTTGATCGCCAAGAGTGTCCCAAACT
ACACACAGGAAGCCTCCTTAGGTGCTCTCCAGAACCTCACAGCCGGAAGTGGACCAATGCCGACATCAGTGGCTCAGACA
GTCGTCCAGAAGGAAAATGGCCTGCAGCACACCCGAAAGATGGTGCATGTCAGTGACCCAAGCGTGAAAAAGACAGCCAA
CTTGCTGCTGAGGAATCTGTCCCAGAATCTTTCTCTGCAGAATGAAATTGCCAAAGAAACTCTCCCCAGTTTGGTCTCCA
TCATTCCTGATACAGTCCCGAGTACTGACCTTCTCATTGAAACTACAGCCCCTGCCTGTTACATGTTGAACAACGTAATC
CAAAACAGTTACCAGAGTGCACAGCACCTTCTAAATACCGGGGGCATCCAGAAAATTATGACCATCAGTGCAGGCGATGC
CTATGCCTCCAACAAAGCAAGTAAAGCTGCTTCCATCCTCCTGTATTCTCTGTAGGCACACACGGAACTCCATCATGCCT
ACAAGAAGGCTCAGTTTAAGAAGACAGATTTTGTCAACAGCTGGACTGTCAAAGCCTACCACTCCCTTAAAGAC
ORF - retro_ptro_657 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 89.77 % |
| Parental protein coverage: | 58.13 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MLEADHMPPSRISAAATFIQHECFQKSEARKRVNQLRGIPKLLQLLKVQNEDVQRAVCGALRNLVFEDND |
| ML.AD.MPPSRISAAATFIQHECFQKSEA.KRVNQ..GIPKLLQLLKVQNEDVQRAV.GALRNL.FEDND | |
| Retrocopy | MLDADQMPPSRISAAATFIQHECFQKSEAGKRVNQFCGIPKLLQLLKVQNEDVQRAVWGALRNLLFEDND |
| Parental | NKLEVAELNGVPRLLQVLKQTRDLETKKQITGLLWNLSSNDKLKNLMITEALLTLTENIIIPFSGWPEGD |
| NKLEVAELNGV.RLLQVLKQTR.LETKKQ.TGLLWNLSSNDKLKNLMITEALL.LTENIII.FSGWPEGD | |
| Retrocopy | NKLEVAELNGVTRLLQVLKQTRVLETKKQLTGLLWNLSSNDKLKNLMITEALLMLTENIIISFSGWPEGD |
| Parental | YPKANGLLDFDIFYNVTGCLRNMSSAGPDGRKAMRRCDGLIDSLVHYVRGTIADYQPDDKATENCVCILH |
| YPKANGLLDFD...N.TGCLRNMS.AGPDGRKAMRR.D.LIDS.VHYVRGTIADYQPDDKA.ENCV.ILH | |
| Retrocopy | YPKANGLLDFDTVCNATGCLRNMSAAGPDGRKAMRRRDRLIDSVVHYVRGTIADYQPDDKAMENCVHILH |
| Parental | NLSYQLEAELPEKYSQNIYIQNRNIQTDNNKSIGCFGSRSRKVKEQYQDVPMPEEKSNPKGVEWLWHSIV |
| NLSYQLE.ELPEKYSQNIYIQN.N.QT.NNKSIGCFGSRSRK.K.QYQD.PMPEEKSNPKGVEWL.HSIV | |
| Retrocopy | NLSYQLEVELPEKYSQNIYIQNPNVQT-NNKSIGCFGSRSRKLKQQYQDMPMPEEKSNPKGVEWL*HSIV |
| Parental | IRMYLSLIAKSVRNYTQEASLGALQNLTAGSGPMPTSVAQTVVQKESGLQHTRKMLHVGDPSVKKTAISL |
| IRMYLSLIAKSV.NYTQEASLGALQNLTAGSGPMPTSVAQTVVQKE.GLQHTRKM.HV.DPSVKKTA..L | |
| Retrocopy | IRMYLSLIAKSVPNYTQEASLGALQNLTAGSGPMPTSVAQTVVQKENGLQHTRKMVHVSDPSVKKTANLL |
| Parental | LRNLSRNLSLQNEIAKETLPDLVSIIPDTVPSTDLLIETTASACYTLNNIIQNSYQNARDLLNTGGIQKI |
| LRNLS.NLSLQNEIAKETLP.LVSIIPDTVPSTDLLIETTA.ACY.LNN.IQNSYQ.A..LLNTGGIQKI | |
| Retrocopy | LRNLSQNLSLQNEIAKETLPSLVSIIPDTVPSTDLLIETTAPACYMLNNVIQNSYQSAQHLLNTGGIQKI |
| Parental | MAISAGDAYASNKASKAASVLLYSLWAHTELHHAYKKAQFKKTDFVNSRTAKAYHSLKD |
| M.ISAGDAYASNKASKAAS.LLYSL.AHTELHHAYKKAQFKKTDFVNS.T.KAYHSLKD | |
| Retrocopy | MTISAGDAYASNKASKAASILLYSL*AHTELHHAYKKAQFKKTDFVNSWTVKAYHSLKD |
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 |
|---|---|---|
| SRP007412_brain_prefrontal_cortex | 0 .00 RPM | 1 .16 RPM |
| SRP007412_cerebellum | 0 .14 RPM | 2 .76 RPM |
| SRP007412_heart | 1 .66 RPM | 148 .00 RPM |
| SRP007412_kidney | 0 .08 RPM | 4 .89 RPM |
| SRP007412_liver | 0 .07 RPM | 10 .80 RPM |
| SRP007412_testis | 0 .42 RPM | 34 .78 RPM |
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_657 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_657 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ptro_657 has 2 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_950 |
| Gorilla gorilla | retro_ggor_766 |
Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Homo sapiens | ENSG00000057294 | 1 retrocopy | |
| Gorilla gorilla | ENSGGOG00000002106 | 1 retrocopy | |
| Nomascus leucogenys | ENSNLEG00000016650 | 1 retrocopy | |
| Pan troglodytes | ENSPTRG00000004820 | 1 retrocopy |
retro_ptro_657 ,
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