RetrogeneDB ID: retro_ggor_1275

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 16:62266938..62268223(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP5A1
• Ensembl ID: ENSGGOG00000016560
• Aliases: None
• Description: ATP synthase subunit alpha [Source:UniProtKB/TrEMBL;Acc:G3RK98]

Sequence

>retro_ggor_1275
AAGGAAGGAGGTATAGTGAAGAGGACAGGAACCATTGTGGACGTTCCAGTTGGTGAGGAGCTGTTGGGTCGTGTAGTTGA
TGCCCTTGGTAATGCTATTGATGGAAAGGGTCCATTTGGTTCGAAGACCCATAAGTGAGTCGGTCTGAAAGCCCCCAGAA
TCATTCCTCGAACTTCAGTGCGGGAACCCATGCCGACTGGCATTAAGGCTGTGGATAGCTTGGTGCCAATTGGTCGTGGT
CAGCATGAGCTGATTATTGGTGACCGAAGGACTGGGAAAACCTCAATTGCTATTGACACAATCATTAACCAGAAACGTTT
CAATGATAGATCTGAAGAAAAGAAGAAGCTGTACTGTATCTATGTTGCTATTGGTCGAAAGAGATCCACTGTTGCTCAGT
TGGTGAAGAGACTTACAGATGCAGATGCCGTGAAGTACACCACTGTGGTGTCTGCTATGGCCTCAGATGCTGCCCTACTT
CAGTACCTGGCTCCTTACTCTGACAGTTCTATGGGAGAGTATTTTAGAGACGATGGCAAATATACTTTGATCATCTATGA
TGACTTATCCCAACAGGCTGTCGCTTACTGTCAGATGTCTCTATTGCTCCACCGACCCCCCTGGTCGTAAGGCCTGTCCT
GGTGATGTGTTTTACCTACACTCCCGGTTGCTGGAGAGAGCAGCCAAAATGAATGATGCTTTTGGTGGTGGCTCCTTGAC
TGCTTTGCTAGTCATAGAAACACAGGCTGGTGATGTGTCTGCTTACATTCCAACGAATGTCATTTCCATCACTGACAGAC
AGATCTTCTTGGAAACAGAATTGTTCTACAAAGATATCCGCTCTGCCATTAACATTGGGTCTGTCTGTGTCTTGTGTTGG
ATCTGCTGCCCAAACCAGGACTATGAAGCAGGTGGCAAGTACCATGAAGCTGGAATTGACTCAGGATCGTGAGGTTGCTG
CTTTTGCCCAGTTTGGTTCTGACCTCGATGCTCCCACTCAACAACTATTGAGTCGCGGTGTGCGTCTAACTGAGTTGCTG
AAGCAAGGACAGTATCCTCCCATGGTTACTGAACAACAAGTGGCTGTTATCTGTGCGGGTGTAAGGGGGTATCTTGATAA
ACTGGAGCCCAGCAAGATTACAAAGTTCGAGAATGCTTTCTTGTCTCATGTTGTCAGCCAGCACTAAGCCCTGTTGGGCA
CTATCAGGGCTGATGGAAAGATCTCAGAAGACTCAGATGCAAAGCTGATGGAGTTGTAACAAATTTCTTGGGTGGATTTG
AAGCT

Alignment

ORF - retro_ggor_1275 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.47 %
• Parental protein coverage: 77.4 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KEGDIVKRTGAIVDVPVGEELLGRVVDALGNTIDGKGPIGSKMRRRVGLKAPGIIPRISVREPMQTGIKA
          KEG.IVKRTG.IVDVPVGEELLGRVVDALGN.IDGKGP.GSK....VGLKAP.IIPR.SVREPM.TGIKA
Retrocopy KEGGIVKRTGTIVDVPVGEELLGRVVDALGNAIDGKGPFGSKTHK*VGLKAPRIIPRTSVREPMPTGIKA

Parental  VDSLVPIGRGQRELIIGDRQTGKTSIAIDTIINQKRFNDGSDEKKKLYCIYVAIGQKRSTVAQLVKRLTD
          VDSLVPIGRGQ.ELIIGDR.TGKTSIAIDTIINQKRFND.S.EKKKLYCIYVAIG.KRSTVAQLVKRLTD
Retrocopy VDSLVPIGRGQHELIIGDRRTGKTSIAIDTIINQKRFNDRSEEKKKLYCIYVAIGRKRSTVAQLVKRLTD

Parental  ADAMKYTIVVSATASDAAPLQYLAPYSGCSMGEYFRDNGKHALIIYDDLSKQAVAYRQMSLLLRR-PPGR
          ADA.KYT.VVSA.ASDAA.LQYLAPYS..SMGEYFRD.GK..LIIYDDLS.QAVAY.QMSLLL.R.PPGR
Retrocopy ADAVKYTTVVSAMASDAALLQYLAPYSDSSMGEYFRDDGKYTLIIYDDLSQQAVAYCQMSLLLHR>PPGR

Parental  EAYPGDVFYLHSRLLERAAKMNDAFGGGSLTALPVIETQAGDVSAYIPTNVISITDGQIFLETELFYKGI
          .A.PGDVFYLHSRLLERAAKMNDAFGGGSLTAL.VIETQAGDVSAYIPTNVISITD.QIFLETELFYK.I
Retrocopy KACPGDVFYLHSRLLERAAKMNDAFGGGSLTALLVIETQAGDVSAYIPTNVISITDRQIFLETELFYKDI

Parental  RPAINV-GLSVSRVGSAAQTRAMKQVAGTMKLELAQYREVAAFAQFGSDLDAATQQLLSRGVRLTELLKQ
          R.AIN..GLSVS.VGSAAQTR.MKQVA.TMKLEL.Q.REVAAFAQFGSDLDA.TQQLLSRGVRLTELLKQ
Retrocopy RSAINI>GLSVSCVGSAAQTRTMKQVASTMKLELTQDREVAAFAQFGSDLDAPTQQLLSRGVRLTELLKQ

Parental  GQYSPMAIEEQVAVIYAGVRGYLDKLEPSKITKFENAFLSHVVSQHQALLGTIRADGKISEQSDAKLKE-
          GQY.PM..E.QVAVI.AGVRGYLDKLEPSKITKFENAFLSHVVSQH.ALLGTIRADGKISE.SDAKL.E.
Retrocopy GQYPPMVTEQQVAVICAGVRGYLDKLEPSKITKFENAFLSHVVSQH*ALLGTIRADGKISEDSDAKLME<

Parental  IVTNFLAGFEA
          .VTNFL.GFEA
Retrocopy VVTNFLGGFEA

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	0.05 RPM	335.39 RPM
SRP007412_cerebellum	0.04 RPM	227.13 RPM
SRP007412_heart	0.16 RPM	404.88 RPM
SRP007412_kidney	0.00 RPM	537.85 RPM
SRP007412_liver	0.05 RPM	145.87 RPM
SRP007412_testis	0.10 RPM	296.40 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_1275 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1275 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1702
Pan troglodytes	retro_ptro_1151
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,