RetrogeneDB ID: retro_ptro_969

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 14:54215501..54215943(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COX5A
• Ensembl ID: ENSPTRG00000007289
• Aliases: None
• Description: Pan troglodytes mitochondrial cytochrome c oxidase subunit Va (COX5A), nuclear gene encoding mitochondrial protein, mRNA. [Source:RefSeq mRNA;Acc:NM_001118913]

Sequence

>retro_ptro_969
GGGGCCGCTCTCCACCGCTGTGCGGTGACTGCAACCGCCCGGGCCGGACCTCGAGGCCTCCTGCATTCCGCCCCAACCCC
CGGCCCCGCCGCGGCTATCCAGTCAGTTCACTGCTATTCCCATGGGTCACGAGACAGATGAGGAGTTTGATGCTCTCTGG
GTAACATACTTCAACAAGCCAGATATAGATGCCTGGCAATTGCGTAAAGGGATGAACACACTTGTTAGCTATGATCTGGT
CCCAGAGCCCAAAATTGTTGATGCTGCTTTGCGGGCATGCAGACGGTTAAACGATTTTGCTAGTGCAGTTGGCATCCTAG
AGGCTGTTAAGGACAAAGCAGGACCTCATAAGGAAATCTACCCCTATGTCATTCAGGAACTCAGACCAACTTTAAATGAA
CTGGGAATCTCCACTCTGGAGGATCTGGGCCTTGACAAAGTG

Alignment

ORF - retro_ptro_969 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.87 %
• Parental protein coverage: 98.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GAALRRCAVAATTRAGPRGLLHSART-PGPAAAIQSVRCYSHGSQETDEEFDARWVTYFNKPDIDAWELR
          GAAL.RCAV.AT.RAGPRGLLHSA.T.P.P............G..ETDEEFDA.WVTYFNKPDIDAW.LR
Retrocopy GAALHRCAVTATARAGPRGLLHSAPT>PAPPRLSSQFTAIPMG-HETDEEFDALWVTYFNKPDIDAWQLR

Parental  KGINTLVTYDMVPEPKIIDAALRACRRLNDFASTVRILEAVKDKAGPHKEIYPYVIQELRPTLNELGIST
          KG.NTLV.YD.VPEPKI.DAALRACRRLNDFAS.V.ILEAVKDKAGPHKEIYPYVIQELRPTLNELGIST
Retrocopy KGMNTLVSYDLVPEPKIVDAALRACRRLNDFASAVGILEAVKDKAGPHKEIYPYVIQELRPTLNELGIST

Parental  PEELGLDKV
          .E.LGLDKV
Retrocopy LEDLGLDKV

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	82.19 RPM
SRP007412_cerebellum	0.00 RPM	32.51 RPM
SRP007412_heart	0.00 RPM	174.38 RPM
SRP007412_kidney	0.00 RPM	84.94 RPM
SRP007412_liver	0.03 RPM	41.87 RPM
SRP007412_testis	0.11 RPM	71.66 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_969 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_969 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_969 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1416

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008643	2 retrocopies	retro_amel_546, retro_amel_706,
Bos taurus	ENSBTAG00000017267	1 retrocopy	retro_btau_711,
Canis familiaris	ENSCAFG00000017977	1 retrocopy	retro_cfam_29,
Choloepus hoffmanni	ENSCHOG00000006108	4 retrocopies	retro_chof_1291, retro_chof_1434, retro_chof_2330, retro_chof_695,
Callithrix jacchus	ENSCJAG00000015613	6 retrocopies	retro_cjac_2567, retro_cjac_3167, retro_cjac_3229, retro_cjac_703, retro_cjac_9, retro_cjac_982,
Cavia porcellus	ENSCPOG00000024832	3 retrocopies	retro_cpor_1248, retro_cpor_770, retro_cpor_970,
Felis catus	ENSFCAG00000010587	3 retrocopies	retro_fcat_1100, retro_fcat_1201, retro_fcat_253,
Homo sapiens	ENSG00000178741	3 retrocopies	retro_hsap_1036, retro_hsap_1337, retro_hsap_1416,
Loxodonta africana	ENSLAFG00000006266	1 retrocopy	retro_lafr_1192,
Macropus eugenii	ENSMEUG00000013942	2 retrocopies	retro_meug_1280, retro_meug_784,
Myotis lucifugus	ENSMLUG00000013702	1 retrocopy	retro_mluc_337,
Macaca mulatta	ENSMMUG00000011677	2 retrocopies	retro_mmul_2176, retro_mmul_2255,
Monodelphis domestica	ENSMODG00000028168	1 retrocopy	retro_mdom_830,
Mustela putorius furo	ENSMPUG00000017314	1 retrocopy	retro_mputfur_652,
Mus musculus	ENSMUSG00000000088	2 retrocopies	retro_mmus_1413, retro_mmus_742,
Otolemur garnettii	ENSOGAG00000005611	5 retrocopies	retro_ogar_1540, retro_ogar_2150, retro_ogar_2432, retro_ogar_2585, retro_ogar_604,
Pan troglodytes	ENSPTRG00000007289	3 retrocopies	retro_ptro_706, retro_ptro_914, retro_ptro_969 ,
Pteropus vampyrus	ENSPVAG00000012957	1 retrocopy	retro_pvam_438,
Rattus norvegicus	ENSRNOG00000018816	1 retrocopy	retro_rnor_1867,
Sarcophilus harrisii	ENSSHAG00000015941	2 retrocopies	retro_shar_238, retro_shar_422,
Tursiops truncatus	ENSTTRG00000008004	2 retrocopies	retro_ttru_161, retro_ttru_765,