RetrogeneDB ID: retro_mmul_238

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:25306300..25308772(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000016657
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: MMU.2609
• Ensembl ID: ENSMMUG00000007001
• Aliases: None
• Description: None

Sequence

>retro_mmul_238
ATGGCAGACCTGAAGTACGGTGTAAAAGTCTATGTCCTGAACGAAGACCAGGAATGGAACAATCTAGGCACCGGTCAGGT
CTCATCCACCTACGACGAGCAGTTCCAGGGCATGTGTCTGCTTGTTCGGTCAGATTCAGATGGGTCAGTCATCCTGCGGT
CACAGATACCTCCAGACAGGCCCTATCGGAAACATGAAGAGACACTAATTGTTTGGTATGAAGCTGAGAACCATGGTTTG
GTGCTGAATTTCCAGGACCCAGCCGGCTGCCAGGATATTTGGAAAGAAATTTGTCAAGTTCAAGGTAAGGATCCGTCTGT
CCAAATCACACAGAACATTTCAGATGAACCAGAAGAAGACTTTGATGAAATGTCAGTAATTGGTAATACGGTTGTGCTGC
CTGACTGTGAACTCAATACACTTGATCAAATTGCTAACATAGTTAACTCAGTTCTCGCCTCACCTATCCGTAGGGAAAGA
CTGGCTCTGATCTTGAAAAATGAGGCTTATATTCAAAAACTACTGCAACTGTTCCACACTTGTGAAAACCTAGAGAACAC
TGAAGGTTTATACCGTTTGCATGAAATTATTAAGGGAATTTTATCCCTCAACAAGTCATGTCTGTTTGAGATAATGTTTT
CTGACGAGTGTATCATGGATGTGGTGGGATGCCTTGAGTATGATCCTGCTTTGGATCAGCCAAAAAGGCATAGGGACTTC
TTGACCAATGATGCAAAGTTCAAGGAAGTTATACCAATAACTAACTCTGAACTTAGGCAAAAAATACATCAGACATACAG
AGTACAGTACATTCATGACATTCTTTTGCCTGTGCCTTCCATATTTGAAGACAATTTTCTTTCTACACTTACAACGTTTA
TTTTATCCAACAAGGCTGAGATAGTAAGCATGCTGCAGAAAGATCACAAATTTTTGTATGAAGTTTTTGCACAGTTAAAG
GATGAGACTACACATGATGATAGACGGTGTGAATTGCTAATTTTTTTCAAGGAATTATGTTCATTTTCTCAGGCATTACA
GCCTCAAAGCAAAGATGCACTATTAGAAACATTGACACAGTTGGGAATTCTTCCTGTTCTTAAAATCATAATGATCAGGG
ATGATTTGCAAGTGAGGTCAGCTGCTGCAGTTATATGTGCTTATCTAGTGGAGTACAGTCCATCCAGGATCCGAGAATTT
ATAATTTCAGAATCCCAGGTGTGCAAAGATAGTGACCTTTTCATTAATGTAATAATTAAACAAATGATCTGTGATACTGA
TCCTGAGTTAGGAGGTGCCGTTCATTTGATGGTAGTTCTCCATACTCTACTTGATCCACGCAACATGCTGACAACACCTG
AGAAAAGTGAAAGAAGTGAATTCCTACATTTCTTCTACAAACATTGCATGCATAAATTTACAGCACCACTTTTGGCCGCC
ACCTCAGAACACAACTGTGAGGAGGATGATATAGTTGGATATGACAAAAACAAAAATTGCCCCAATAATAATCAAACAGC
ACAACTGCTTGCTTTGATTTTGGAGCTACTTACATTTTGTATACAACATCATACATACTACATAAGAAACTATATCTTGA
ACAAAGACTTGCTAAGAAAGGCCTTGATATTGACGAATTCAAAGCATACTCACCTGATTTTGTGTGCTCTTCGCTTTATG
AGAAGGATGATCAGCCTTAATGATGAAATTTATAATAATTACATCATCAAGGGAAATCATTTTGAGCCAGTTGTAAATGC
TCTTCTAGATAATGGAACTCGGTATAATATGTTGAATTCAGCTATTCTTGAGCTATTTGAATACATAAGAGTGGAAAATA
TCAAGTCTCTTGTTTCACATATAGTTGAAAAGTTTTATAACACACTTGAATCGATTGAATATGTTCAGACATTCAAAGGA
TTGAAGATTAAATATGAAAAAGAGAGAGACAGACAAAGTCAAATACAGAAGAATTTACATTCTGTACTGCAAAATATGGT
AGTTTGCACAGGTACCATAGAAGAAATGGAGCTGAAAGAAGAAATATGTTTTATGGAAGATGCAGAAGAAGCAGTTATGC
CACCACTGGAAGATGATGATGAATTTATCGAGACTAAAAGAACCCAAGAAGGAGAAGCAGTTATGCCACCACTGGAAGAT
GATGATGAATTTATGGAGACTAAAAGAACCCAAGAAGGAGAAGCAGTTATGCTACCACTGGAAGATGACGATGAATTTAT
GGAGACTAAAAGAACCCAAGAACATGAAGACAAAGTAGACTCTCCCAAAAGAACATCTTCTGGTGATTTCAAATTCTCTT
CATCTTATTCTGCTTGTGCTGCTATTGGAACAGGTAGCCCAAGTGGTAGCAGTGTGGTTCGTTTAGTGGATCATCCAGAT
GATGAAGAAGAAAAACAAGAAGATAAAGAAGATGAAACATCCCCCAAGAAGAAACCTCGTCCTAGCTCCTAA

Alignment

ORF - retro_mmul_238 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.37 %
• Parental protein coverage: 81.64 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSDTRRRVKVYTLNEDRQWDDRGTGHVSSTYVEELKGMSLLVRAESDGSLLLESKINPNTAYQKQQDTLI
          M.D....VKVY.LNED..W...GTG.VSSTY.E...GM.LLVR..SDGS..L.S.I.P...Y.K...TLI
Retrocopy MADLKYGVKVYVLNEDQEWNNLGTGQVSSTYDEQFQGMCLLVRSDSDGSVILRSQIPPDRPYRKHEETLI

Parental  VWSEAENYDLALSFQEKAGCDEIWEKICQVQGKDPSVEVTQDLIDESEEERFEEMPETSHLIDLPTCELN
          VW.EAEN..L.L.FQ..AGC..IW..ICQVQGKDPSV..TQ...DE.EE..F.EM........LP.CELN
Retrocopy VWYEAENHGLVLNFQDPAGCQDIWKEICQVQGKDPSVQITQNISDEPEED-FDEMSVIGNTVVLPDCELN

Parental  KLEEIADLVTSVLSSPIRREKLALALENEGYIKKLLQLFQACENLENTEGLHHLYEIIRGILFLNKATLF
          .L..IA..V.SVL.SPIRRE.LAL.L.NE.YI.KLLQLF..CENLENTEGL..L.EII.GIL.LNK..LF
Retrocopy TLDQIANIVNSVLASPIRRERLALILKNEAYIQKLLQLFHTCENLENTEGLYRLHEIIKGILSLNKSCLF

Parental  EVMFSDECIMDVVGCLEYDPALAQPKRHREFLTKTAKFKEVIPITDSELRQKIHQTYRVQYIQDIILPTP
          E.MFSDECIMDVVGCLEYDPAL.QPKRHR.FLT..AKFKEVIPIT.SELRQKIHQTYRVQYI.DI.LP.P
Retrocopy EIMFSDECIMDVVGCLEYDPALDQPKRHRDFLTNDAKFKEVIPITNSELRQKIHQTYRVQYIHDILLPVP

Parental  SVFEENFLSTLTSFIFFNKVEIVSMLQEDEKFLSEVFAQLTDEATDDDKRRELVNFFKEFCAFSQTLQPQ
          S.FE.NFLSTLT.FI..NK.EIVSMLQ.D.KFL.EVFAQL.DE.T.DD.R.EL..FFKE.C.FSQ.LQPQ
Retrocopy SIFEDNFLSTLTTFILSNKAEIVSMLQKDHKFLYEVFAQLKDETTHDDRRCELLIFFKELCSFSQALQPQ

Parental  NRDAFFKTLAKLGILPALEIVMGMDDLQVRSAATDIFSYLVEFSPSMVREFVMQEAQQSDDDILLINVVI
          ..DA...TL..LGILP.L.I.M..DDLQVRSAA..I..YLVE.SPS..REF...E.Q...D..L.INV.I
Retrocopy SKDALLETLTQLGILPVLKIIMIRDDLQVRSAAAVICAYLVEYSPSRIREFIISESQVCKDSDLFINVII

Parental  EQMICDTDPELGGAVQLMGLLRTLIDPENMLATTNKTEKSEFLNFFYNHCMHVLTAPLLTNTSKDKCEKD
          .QMICDTDPELGGAV.LM..L.TL.DP.NML.T..K.E.SEFL.FFY.HCMH..TAPLL..TS...CE.D
Retrocopy KQMICDTDPELGGAVHLMVVLHTLLDPRNMLTTPEKSERSEFLHFFYKHCMHKFTAPLLAATSEHNCEED

Parental  NIVGSNKNNTICPDNYQTAQLLALILELLTFCVEHHTYHIKNYIMNKDLLRRVLVLMNSKHTFLALCALR
          .IVG..KN...CP.N.QTAQLLALILELLTFC..HHTY.I.NYI.NKDLLR..L.L.NSKHT.L.LCALR
Retrocopy DIVGYDKNKN-CPNNNQTAQLLALILELLTFCIQHHTYYIRNYILNKDLLRKALILTNSKHTHLILCALR

Parental  FMRRIIGLKDEFYNRYITKGNLFEPVINALLDNGTRYNLLNSAVIELFEFIRVEDIKSLTAHIVENFYKA
          FMRR.I.L.DE.YN.YI.KGN.FEPV.NALLDNGTRYN.LNSA..ELFE.IRVE.IKSL..HIVE.FY..
Retrocopy FMRRMISLNDEIYNNYIIKGNHFEPVVNALLDNGTRYNMLNSAILELFEYIRVENIKSLVSHIVEKFYNT

Parental  LESIEYVQTFKGLKTKYEQEKDRQNQKLNSVPSILRS
          LESIEYVQTFKGLK.KYE.E.DRQ.Q......S.L..
Retrocopy LESIEYVQTFKGLKIKYEKERDRQSQIQKNLHSVLQN

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	0.00 RPM	58.71 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	39.67 RPM
SRP007412_cerebellum	0.00 RPM	71.68 RPM
SRP007412_heart	0.00 RPM	22.67 RPM
SRP007412_kidney	0.00 RPM	46.48 RPM
SRP007412_liver	0.00 RPM	16.94 RPM
SRP007412_testis	6.75 RPM	51.45 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_238 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_238 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_238 has 7 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4799
Pan troglodytes	retro_ptro_3191
Oryctolagus cuniculus	retro_ocun_9
Bos taurus	retro_btau_232
Sus scrofa	retro_sscr_1187
Canis familiaris	retro_cfam_226
Equus caballus	retro_ecab_23

---

Parental genes homology:

Parental genes homology involve 18 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003843	1 retrocopy	retro_amel_48,
Bos taurus	ENSBTAG00000000545	1 retrocopy	retro_btau_232,
Canis familiaris	ENSCAFG00000002860	1 retrocopy	retro_cfam_226,
Equus caballus	ENSECAG00000013819	1 retrocopy	retro_ecab_23,
Echinops telfairi	ENSETEG00000002420	1 retrocopy	retro_etel_1699,
Felis catus	ENSFCAG00000026457	1 retrocopy	retro_fcat_13,
Homo sapiens	ENSG00000138041	1 retrocopy	retro_hsap_4799,
Loxodonta africana	ENSLAFG00000017825	1 retrocopy	retro_lafr_791,
Myotis lucifugus	ENSMLUG00000003875	1 retrocopy	retro_mluc_994,
Macaca mulatta	ENSMMUG00000007001	1 retrocopy	retro_mmul_238 ,
Mustela putorius furo	ENSMPUG00000002435	1 retrocopy	retro_mputfur_92,
Nomascus leucogenys	ENSNLEG00000009338	1 retrocopy	retro_nleu_1112,
Oryctolagus cuniculus	ENSOCUG00000006880	1 retrocopy	retro_ocun_9,
Otolemur garnettii	ENSOGAG00000009837	1 retrocopy	retro_ogar_140,
Pan troglodytes	ENSPTRG00000011933	1 retrocopy	retro_ptro_3191,
Sus scrofa	ENSSSCG00000008398	1 retrocopy	retro_sscr_1187,
Ictidomys tridecemlineatus	ENSSTOG00000006276	1 retrocopy	retro_itri_63,
Tursiops truncatus	ENSTTRG00000000027	1 retrocopy	retro_ttru_1397,