RetrogeneDB ID: retro_ptro_1151

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 16:71367486..71368768(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP5A1
• Ensembl ID: ENSPTRG00000009991
• Aliases: None
• Description: Pan troglodytes ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1, cardiac muscle (ATP5A1), nuclear gene encoding mitochondrial protein, mRNA. [Source:RefSeq mRNA;Acc:NM_001135736]

Sequence

>retro_ptro_1151
AAGGAAGGAGGTATAGTGAAGAGGACAGGAACCATTGTGGACGTTCCAGTCGGTGAGGAGCTGTTGGGTCGTGTAGTTGA
TGCCCTTGGTAATGCTATTGATGGAAAGGGTCCAATGGGTTCCAAGACCCATAAGTGAGTCGGTCTGAAAGCCCCCAGAA
TCATTCCTCGAACTTCAGTGTGGGAACCCATGCCGACTGGCATTAAGGCTGTGGATAGCTTGGTGCCAATTGGTCGTGGT
CAGCATGAGCTGATTATTGGTGACCGAAGGACTGGGAAAACCTCAATTGCTATTGACACAATCATTAACCAGAAACATTT
CAATGATAGATCTGAAGAAAAGAAGAAGCTGTACTGTATCTATGTTGCTATTGGTCGAAAGAGATCCACTGTTGCTCAGT
TGGTGAAGAGACTTACAGATGCAGATGCCGTGAAGTACACCACTGTGGTGTCAACTATGGCCTCAGATGCTGCCCTACTT
CAGTACCTGGCTCCTTACTCTGACTGTTCCATGAGAGAGTATTTTAGAGACGATGGCAAATATACTTTGATCATCTATGA
CGACTTATCCAAACAGGCTGTCGCTTACTGTCAGATGTCTCTGTTGCTCCACCGACCCCCCTGGTCGTAAGGCCTGTCCT
GGTGATGTGTTTTACCTACACTCCCGGTTGCTGGAGAGAGCAGCCAAAATGAATGATGCTTTTGGTGGTGGCTCCTTGAC
TGCTTTGCTAGTCATAGAAACACAGGCTGATGATGTGTCTGCTTACATTCCAACGAATGTCATTTCCATCACTGACAGAC
AGATCTTGGAAACAGAATTGTTCTACAAAGATATCCGCTCTGCCATTAACATTGGGTCTGTCTGTGTCTTGTGTTGGATC
TGCTGCCCAAACCAGGACTATGAAGCAGGCGGCAGGTACCATGAAGCTGGAATTGGCTCAGGATCGTGAGGTTGCTGCTT
TTGCCCAGTTTGGTTCTGACCTCGATGCTCCCACTCAACAACTATTGAGTCACAGTGTGCGTCTAACTGAGTTGCTGAAG
CAAGGACAGTATCCTCCCATGGTTACTGAACAACAAGTGGCTGTTATCTGTGCGGGTGTAAGGGGGTATCTTGATAAACT
GGAGCCCAGCAAGATTACAAAGTTTGAGAATGCTTTCTTGTCTCATGTTGTCAGCCAGCGCTAAGCCCTGTTGGGCACTA
TCAGGGCTGATGGAAAGATCTCAGAAGACTCAGATGCAAAGCTGATGGAGTTGTAACAAATTTCTTGGCTGGATTTGAAG
CT

Alignment

ORF - retro_ptro_1151 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.77 %
• Parental protein coverage: 77.4 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KEGDIVKRTGAIVDVPVGEELLGRVVDALGNAIDGKGPIGSKTRRRVGLKAPGIIPRISVREPMQTGIKA
          KEG.IVKRTG.IVDVPVGEELLGRVVDALGNAIDGKGP.GSKT...VGLKAP.IIPR.SV.EPM.TGIKA
Retrocopy KEGGIVKRTGTIVDVPVGEELLGRVVDALGNAIDGKGPMGSKTHK*VGLKAPRIIPRTSVWEPMPTGIKA

Parental  VDSLVPIGRGQRELIIGDRQTGKTSIAIDTIINQKRFNDGSDEKKKLYCIYVAIGQKRSTVAQLVKRLTD
          VDSLVPIGRGQ.ELIIGDR.TGKTSIAIDTIINQK.FND.S.EKKKLYCIYVAIG.KRSTVAQLVKRLTD
Retrocopy VDSLVPIGRGQHELIIGDRRTGKTSIAIDTIINQKHFNDRSEEKKKLYCIYVAIGRKRSTVAQLVKRLTD

Parental  ADAMKYTIVVSATASDAAPLQYLAPYSGCSMGEYFRDNGKHALIIYDDLSKQAVAYRQMSLLLRR-PPGR
          ADA.KYT.VVS..ASDAA.LQYLAPYS.CSM.EYFRD.GK..LIIYDDLSKQAVAY.QMSLLL.R.PPGR
Retrocopy ADAVKYTTVVSTMASDAALLQYLAPYSDCSMREYFRDDGKYTLIIYDDLSKQAVAYCQMSLLLHR>PPGR

Parental  EAYPGDVFYLHSRLLERAAKMNDAFGGGSLTALPVIETQAGDVSAYIPTNVISITDGQIFLETELFYKGI
          .A.PGDVFYLHSRLLERAAKMNDAFGGGSLTAL.VIETQA.DVSAYIPTNVISITD.QI.LETELFYK.I
Retrocopy KACPGDVFYLHSRLLERAAKMNDAFGGGSLTALLVIETQADDVSAYIPTNVISITDRQI-LETELFYKDI

Parental  RPAINV-GLSVSRVGSAAQTRAMKQVAGTMKLELAQYREVAAFAQFGSDLDAATQQLLSRGVRLTELLKQ
          R.AIN..GLSVS.VGSAAQTR.MKQ.AGTMKLELAQ.REVAAFAQFGSDLDA.TQQLLS..VRLTELLKQ
Retrocopy RSAINI>GLSVSCVGSAAQTRTMKQAAGTMKLELAQDREVAAFAQFGSDLDAPTQQLLSHSVRLTELLKQ

Parental  GQYSPMAIEEQVAVIYAGVRGYLDKLEPSKITKFENAFLSHVVSQHQALLGTIRADGKISEQSDAKLKE-
          GQY.PM..E.QVAVI.AGVRGYLDKLEPSKITKFENAFLSHVVSQ..ALLGTIRADGKISE.SDAKL.E.
Retrocopy GQYPPMVTEQQVAVICAGVRGYLDKLEPSKITKFENAFLSHVVSQR*ALLGTIRADGKISEDSDAKLME<

Parental  IVTNFLAGFEA
          .VTNFLAGFEA
Retrocopy VVTNFLAGFEA

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	0.46 RPM	411.90 RPM
SRP007412_cerebellum	0.47 RPM	448.82 RPM
SRP007412_heart	0.32 RPM	1023.88 RPM
SRP007412_kidney	0.18 RPM	788.29 RPM
SRP007412_liver	0.20 RPM	218.17 RPM
SRP007412_testis	0.00 RPM	173.67 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1151 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1151 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1151 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1702
Gorilla gorilla	retro_ggor_1275
Pongo abelii	retro_pabe_1363

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002507	2 retrocopies	retro_btau_1380, retro_btau_1426,
Canis familiaris	ENSCAFG00000017648	2 retrocopies	retro_cfam_1483, retro_cfam_516,
Dasypus novemcinctus	ENSDNOG00000006331	2 retrocopies	retro_dnov_1740, retro_dnov_2525,
Equus caballus	ENSECAG00000021561	1 retrocopy	retro_ecab_788,
Homo sapiens	ENSG00000152234	1 retrocopy	retro_hsap_1702,
Gorilla gorilla	ENSGGOG00000016560	1 retrocopy	retro_ggor_1275,
Meleagris gallopavo	ENSMGAG00000009963	1 retrocopy	retro_mgal_14,
Microcebus murinus	ENSMICG00000017500	1 retrocopy	retro_mmur_1210,
Myotis lucifugus	ENSMLUG00000009856	1 retrocopy	retro_mluc_1198,
Macaca mulatta	ENSMMUG00000003570	1 retrocopy	retro_mmul_1208,
Mustela putorius furo	ENSMPUG00000000923	1 retrocopy	retro_mputfur_601,
Nomascus leucogenys	ENSNLEG00000010973	1 retrocopy	retro_nleu_1334,
Pongo abelii	ENSPPYG00000009130	1 retrocopy	retro_pabe_1363,
Pan troglodytes	ENSPTRG00000009991	1 retrocopy	retro_ptro_1151 ,
Sarcophilus harrisii	ENSSHAG00000017177	1 retrocopy	retro_shar_109,
Tarsius syrichta	ENSTSYG00000007804	1 retrocopy	retro_tsyr_1186,
Tursiops truncatus	ENSTTRG00000005118	1 retrocopy	retro_ttru_159,