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 symbol: PKP2
• Ensembl ID: ENSPTRG00000004820
• Aliases: None
• Description: plakophilin 2 [Source:HGNC Symbol;Acc:9024]

Sequence

>retro_ptro_657
ATGCTCGATGCAGACCAGATGCCGCCGTCCAGGATTTCTGCCGCAGCCACTTTCATACAGCACGAGTGCTTCCAGAAATC
TGAAGCTGGGAAGAGGGTTAACCAGTTTTGTGGCATCCCCAAGCTTCTGCAGCTCCTAAAAGTTCAGAATGAAGATGTTC
AGCGAGCTGTGTGGGGGGCCTTGAGAAACTTACTATTTGAAGACAATGACAACAAATTGGAGGTGGCTGAACTAAATGGG
GTAACTCGGCTGCTCCAGGTGCTGAAGCAAACCAGAGTCTTGGAGACTAAAAAACAACTAACAGGTTTGCTGTGGAATTT
GTCATCTAATGACAAACTCAAGAATCTCATGATAACAGAAGCATTGCTTATGCTGACCGAGAATATAATCATCTCCTTTT
CTGGATGGCCTGAAGGAGACTACCCAAAAGCGAATGGTTTGCTCGATTTTGACACAGTCTGCAACGCCACTGGATGTCTA
AGAAACATGAGTGCTGCTGGCCCTGATGGGAGAAAAGCAATGAGAAGACGTGACCGACTCATTGACTCAGTGGTCCATTA
TGTCAGAGGAACCATTGCGGATTACCAGCCAGATGACAAGGCCATGGAGAATTGTGTGCACATTCTTCATAACCTCTCCT
ACCAGCTGGAGGTAGAGCTCCCAGAGAAATATTCCCAGAATATCTATATTCAAAACCCAAATGTCCAGACTAACAACAAA
AGTATTGGATGTTTTGGCAGTCGAAGCAGGAAACTAAAACAGCAATACCAGGACATGCCGATGCCAGAGGAAAAGAGCAA
CCCCAAGGGCGTGGAGTGGCTGTGACACTCCATCGTGATAAGGATGTATCTGTCCTTGATCGCCAAGAGTGTCCCAAACT
ACACACAGGAAGCCTCCTTAGGTGCTCTCCAGAACCTCACAGCCGGAAGTGGACCAATGCCGACATCAGTGGCTCAGACA
GTCGTCCAGAAGGAAAATGGCCTGCAGCACACCCGAAAGATGGTGCATGTCAGTGACCCAAGCGTGAAAAAGACAGCCAA
CTTGCTGCTGAGGAATCTGTCCCAGAATCTTTCTCTGCAGAATGAAATTGCCAAAGAAACTCTCCCCAGTTTGGTCTCCA
TCATTCCTGATACAGTCCCGAGTACTGACCTTCTCATTGAAACTACAGCCCCTGCCTGTTACATGTTGAACAACGTAATC
CAAAACAGTTACCAGAGTGCACAGCACCTTCTAAATACCGGGGGCATCCAGAAAATTATGACCATCAGTGCAGGCGATGC
CTATGCCTCCAACAAAGCAAGTAAAGCTGCTTCCATCCTCCTGTATTCTCTGTAGGCACACACGGAACTCCATCATGCCT
ACAAGAAGGCTCAGTTTAAGAAGACAGATTTTGTCAACAGCTGGACTGTCAAAGCCTACCACTCCCTTAAAGAC

Alignment

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

Expression

RNA-Seq

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

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_657 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_657 was not experimentally validated.

Homology

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

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000057294	1 retrocopy	retro_hsap_950,
Gorilla gorilla	ENSGGOG00000002106	1 retrocopy	retro_ggor_766,
Nomascus leucogenys	ENSNLEG00000016650	1 retrocopy	retro_nleu_786,
Pan troglodytes	ENSPTRG00000004820	1 retrocopy	retro_ptro_657 ,