RetrogeneDB ID: retro_ptro_1931

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:146413052..146413569(-)
• Located in intron of: ENSPTRG00000015486

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: RPL8
• Ensembl ID: ENSPTRG00000020716
• Aliases: None
• Description: ribosomal protein L8 [Source:HGNC Symbol;Acc:10368]

Sequence

>retro_ptro_1931
GGCCAGTTTGTGTATTGCGGCAGGAAGGCCCAGCTCAACATTGGCAGTGTGCTCCCTGTGGGCACCATGCCTGAGGGTAT
GATCGAGTGCTGCCTGGAGGAGAAACCTGGAGGCCGTAGCAAGCTGTCCTGGGCATCAGGGAACTATGCCACTGCTATCT
CCCACAACCCTGAGACCAGAAGACCCGTGTGAAGCTGCCCTCTGGCTCCAAGAAGGTTATCTCCTCAGCCAACAGAGCTG
TGGCTGGTGTGGTGGCTGGAGGTGGCCGAACTGACAAACCCATCTTGAAGGCTTGCCAAGCCTACCACAAATATAAGGCA
AAGAGGAACTGGTGGCCACGAGTATGGGATGTGGCCATGAACCCTATGGAGCATCCTTTTGGAGGTGGCAACCACCAGCA
CATCGGCATCCCCTCCGCCATCTCAGAGATGACCCTGCTGGCTGCAAAATGGGTCTCATTGCTGCCCGCCAGACTGGACG
TCTCTGGGGAACCAAGACTGTGCAGGAGAAAGAGAAC

Alignment

ORF - retro_ptro_1931 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84. %
• Parental protein coverage: 67.32 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GQFVYCGKKAQLNIGNVLPVGTMPEGTIVCCLEEKPGDRGKLARASGNYATVISHNPETK-KTRVKLPSG
          GQFVYCG.KAQLNIG.VLPVGTMPEG.I.CCLEEKPG.R.KL..ASGNYAT.ISHNPET..KTRVKLPSG
Retrocopy GQFVYCGRKAQLNIGSVLPVGTMPEGMIECCLEEKPGGRSKLSWASGNYATAISHNPETR<KTRVKLPSG

Parental  SKKVISSANRAVVGVVAGGGRIDKPILKAGRAYHKYKAKRNCWPRVRGVAMNPVEHPFGGGNHQHIGKPS
          SKKVISSANRAV.GVVAGGGR.DKPILKA..AYHKYKAKRN.WPRV..VAMNP.EHPFGGGNHQHIG.PS
Retrocopy SKKVISSANRAVAGVVAGGGRTDKPILKACQAYHKYKAKRNWWPRVWDVAMNPMEHPFGGGNHQHIGIPS

Parental  TIR-RDAPAGRKVGLIAARRTGRLRGTKTVQEKEN
          .I..RD.PAG.K.GLIAAR.TGRL.GTKTVQEKEN
Retrocopy AIS<RDDPAGCKMGLIAARQTGRLWGTKTVQEKEN

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	0.04 RPM	307.06 RPM
SRP007412_cerebellum	0.00 RPM	434.88 RPM
SRP007412_heart	0.00 RPM	268.76 RPM
SRP007412_kidney	0.03 RPM	760.08 RPM
SRP007412_liver	0.10 RPM	783.46 RPM
SRP007412_testis	0.21 RPM	130.78 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1931 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1931 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1931 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2851
Gorilla gorilla	retro_ggor_1974
Macaca mulatta	retro_mmul_1470

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000017933	1 retrocopy	retro_acar_31,
Bos taurus	ENSBTAG00000026327	1 retrocopy	retro_btau_96,
Dasypus novemcinctus	ENSDNOG00000009300	2 retrocopies	retro_dnov_2505, retro_dnov_503,
Gorilla gorilla	ENSGGOG00000008164	1 retrocopy	retro_ggor_1974,
Macaca mulatta	ENSMMUG00000013379	2 retrocopies	retro_mmul_1470, retro_mmul_1531,
Mustela putorius furo	ENSMPUG00000006022	1 retrocopy	retro_mputfur_1517,
Mus musculus	ENSMUSG00000003970	2 retrocopies	retro_mmus_2004, retro_mmus_2112,
Oryctolagus cuniculus	ENSOCUG00000024716	1 retrocopy	retro_ocun_146,
Pan troglodytes	ENSPTRG00000020716	1 retrocopy	retro_ptro_1931 ,
Rattus norvegicus	ENSRNOG00000048523	2 retrocopies	retro_rnor_122, retro_rnor_239,