RetrogeneDB ID: retro_mmul_1659

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:189696275..189697043(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000015967
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MMU.4027
• Ensembl ID: ENSMMUG00000003313
• Aliases: None
• Description: ATP synthase, H+ transporting, mitochondrial Fo complex, subunit B1 [Source:RefSeq peptide;Acc:NP_001247608]

Sequence

>retro_mmul_1659
ATGCTGTCCCGGGTGGAACTTTCTGCCACTGCCACAGCGGCCCCCTCTCTGAATAATGCAGCCTTCCTAGGTCCAGCGGT
ATTGCAGGCAACAAGGACCTTTCACGCAGGCAGCCACACCTTGGCCCTCTACCACCTTTCCCTGAATGTGGAGGAAAAGT
TCGTCTTGGACTGATCCTTGAGGAATTCTTCAAGTTTCTTTATCTTAAAGCTGGTGTAACAGGACCTTATGTGCTCAGAA
CTAGGCTTATCCGGTATCCTTTATCCAAAGAAATATATGTGATTATTGCAGAGACCTTCTCAACCATATTAGTAGTAGCG
TTACTTGTCTATGCAATTAAAAAATATGGTGCCTCTGTTGCAGAATTTGCTGATAAACTCAATGAGCAAAAACTTGCCCA
ACTAGAAGAGGCGAAGCAGGCTTCCATCCAACAAATCCAGGATGCAATTGATTTGGAGAAGTCACAGCAGGCACTGGTTC
AGAAGCTCCATTACCTTTTCGATGTGCAGAGGAATAACACTGCTGTGGCTTTGGAAGTTACTTACCAGGAACGACTGTAT
AAAGTATATAAGGAAGTAAAGAATCGCCGGGACTATCATATATCTGTGCAGAACATGATGCGTCGAAAGGAACAACCAGC
ACATGATAAATTGGGTGGAGAAGCACGTGGTGCAGAGCATCTCTGCACAGCAGAAAAAGGAGATAACTGCTAAGTGCATT
GCGGACCTCAAGCTTCTGGCAAAGAAGGCTCAAGCACAGCCAGTTATG

Alignment

ORF - retro_mmul_1659 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.91 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MLSRVVLSAAATAAPSLKNAAFLGPGVLQATRTFHTG-QPHLAPIPPLPEYGGKVRYGLIPEEFFQFLYP
          MLSRV.LSA.ATAAPSL.NAAFLGP.VLQATRTFH.G.QPHL.P.PP.PE.GGKVR.GLI.EEFF.FLY.
Retrocopy MLSRVELSATATAAPSLNNAAFLGPAVLQATRTFHAG<QPHLGPLPPFPECGGKVRLGLILEEFFKFLYL

Parental  KTGVTGPYVLGTGLILYALSKEIYVITAETFTAMSLIGIMVYGIKKYGPTVAAYADKINEQKLAQLEEAK
          K.GVTGPYVL.T.LI.Y.LSKEIYVI.AETF.........VY.IKKYG..VA..ADK.NEQKLAQLEEAK
Retrocopy KAGVTGPYVLRTRLIRYPLSKEIYVIIAETFSTILVVALLVYAIKKYGASVAEFADKLNEQKLAQLEEAK

Parental  QSSIQQMQNAIDTEKSQQALTQKRHYLFDVQRNNIAMALEVTYRERLYRVYKEVKSRLDYHIAVQNMTRR
          Q.SIQQ.Q.AID.EKSQQAL.QK.HYLFDVQRNN.A.ALEVTY.ERLY.VYKEVK.R.DYHI.VQNM.RR
Retrocopy QASIQQIQDAIDLEKSQQALVQKLHYLFDVQRNNTAVALEVTYQERLYKVYKEVKNRRDYHISVQNMMRR

Parental  KEQ-EHMINWVEKHVVQSISAEQEKETVAKCIADLKLLAKKAQAPLVM
          KEQ..HMINWVEKHVVQSISA.Q.KE..AKCIADLKLLAKKAQA..VM
Retrocopy KEQ>QHMINWVEKHVVQSISAQQKKEITAKCIADLKLLAKKAQAQPVM

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	0.67 RPM	54.79 RPM
SRP007412_brain_prefrontal_cortex	1.27 RPM	59.89 RPM
SRP007412_cerebellum	0.58 RPM	51.08 RPM
SRP007412_heart	0.18 RPM	78.32 RPM
SRP007412_kidney	0.70 RPM	75.47 RPM
SRP007412_liver	0.00 RPM	51.74 RPM
SRP007412_testis	0.19 RPM	49.57 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1659 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1659 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1659 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3812
Pan troglodytes	retro_ptro_2586
Gorilla gorilla	retro_ggor_2564
Pongo abelii	retro_pabe_3111

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Parental genes homology:

Parental genes homology involve 26 parental genes, and 77 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005433	1 retrocopy	retro_amel_1118,
Bos taurus	ENSBTAG00000006441	1 retrocopy	retro_btau_745,
Callithrix jacchus	ENSCJAG00000013353	9 retrocopies	retro_cjac_1943, retro_cjac_2270, retro_cjac_2482, retro_cjac_2747, retro_cjac_2815, retro_cjac_2854, retro_cjac_3067, retro_cjac_528, retro_cjac_833,
Cavia porcellus	ENSCPOG00000014070	3 retrocopies	retro_cpor_1120, retro_cpor_448, retro_cpor_563,
Equus caballus	ENSECAG00000018599	1 retrocopy	retro_ecab_494,
Echinops telfairi	ENSETEG00000010713	3 retrocopies	retro_etel_105, retro_etel_1784, retro_etel_408,
Felis catus	ENSFCAG00000028321	1 retrocopy	retro_fcat_1012,
Homo sapiens	ENSG00000116459	6 retrocopies	retro_hsap_1705, retro_hsap_1951, retro_hsap_3673, retro_hsap_3762, retro_hsap_3812, retro_hsap_828,
Gorilla gorilla	ENSGGOG00000005215	6 retrocopies	retro_ggor_1279, retro_ggor_1721, retro_ggor_2482, retro_ggor_2530, retro_ggor_2564, retro_ggor_678,
Loxodonta africana	ENSLAFG00000004809	1 retrocopy	retro_lafr_602,
Microcebus murinus	ENSMICG00000011992	1 retrocopy	retro_mmur_846,
Myotis lucifugus	ENSMLUG00000012417	1 retrocopy	retro_mluc_2184,
Macaca mulatta	ENSMMUG00000003313	3 retrocopies	retro_mmul_1086, retro_mmul_1659 , retro_mmul_1791,
Mus musculus	ENSMUSG00000000563	2 retrocopies	retro_mmus_2215, retro_mmus_791,
Nomascus leucogenys	ENSNLEG00000003971	8 retrocopies	retro_nleu_172, retro_nleu_2090, retro_nleu_2153, retro_nleu_2154, retro_nleu_2546, retro_nleu_260, retro_nleu_524, retro_nleu_975,
Oryctolagus cuniculus	ENSOCUG00000007809	1 retrocopy	retro_ocun_25,
Otolemur garnettii	ENSOGAG00000011486	3 retrocopies	retro_ogar_2102, retro_ogar_2295, retro_ogar_2887,
Pongo abelii	ENSPPYG00000001032	3 retrocopies	retro_pabe_2056, retro_pabe_3012, retro_pabe_3111,
Pan troglodytes	ENSPTRG00000001099	5 retrocopies	retro_ptro_1154, retro_ptro_1305, retro_ptro_2553, retro_ptro_2586, retro_ptro_578,
Pteropus vampyrus	ENSPVAG00000010604	3 retrocopies	retro_pvam_1061, retro_pvam_1110, retro_pvam_283,
Sorex araneus	ENSSARG00000002107	3 retrocopies	retro_sara_424, retro_sara_428, retro_sara_610,
Sarcophilus harrisii	ENSSHAG00000013185	1 retrocopy	retro_shar_700,
Ictidomys tridecemlineatus	ENSSTOG00000007630	3 retrocopies	retro_itri_1146, retro_itri_1219, retro_itri_503,
Tarsius syrichta	ENSTSYG00000000420	5 retrocopies	retro_tsyr_1226, retro_tsyr_1553, retro_tsyr_1852, retro_tsyr_502, retro_tsyr_511,
Tursiops truncatus	ENSTTRG00000001546	1 retrocopy	retro_ttru_1654,
Vicugna pacos	ENSVPAG00000000206	2 retrocopies	retro_vpac_154, retro_vpac_319,