RetrogeneDB ID: retro_mmul_973

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 12:100278148..100279082(-)
• Located in intron of: ENSMMUG00000017404

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL3
• Ensembl ID: ENSMMUG00000010029
• Aliases: None
• Description: ribosomal protein L3 [Source:RefSeq peptide;Acc:NP_001180483]

Sequence

>retro_mmul_973
CCTCAAGGCCTACAGACCTCCAAGACCATCTTTGCTAAGCACATCAGCAATGAGTGCAAAAAGCACTTCTCTAAGAACTG
ACATAAATCTAAGAAGAAGGCCTTTACCAGTTACTGCAAGAAATGGCAGAATAAGGATAGCAAGAAGCAGCTGGAGCAAG
ACTTCAGCAGCATGAAGAAGTACTGCCAAGTCATCCACGTCACTGCCCACACCCACATGCACCTGCTTCCTGTGCGCCAG
AAGAAGGCCCCGCTGATGGAGATCCAGGTGAACAGAGGCACCGTGGCCAAGAAGCTGGACTGGGACCGGGAGAGGCTAGA
ACAGCAGGTACCTGTGAACCAAGTGTTTGGGCAGGATGAGATGATTGACATCTTCAAGGTGACCAAGGGCAAAGACTACA
AAGGGGTCACAAGTCATTGGCATGCCAAGAAGCTACCCTGCAAGACCCAATGAGGCCTGTGCAAGGTGGCCTGGATTGGG
GCATGGCATCCTGCCTGTGTGGACCTTCTCTGTGGCATGCACTGGACAGAAAGGCTACCATCACCACACTACAAGAAGAT
CAATCTGTATGACCGGCCAGGGCTACCTTATCAAGGACGACAAACTGATCAAGAACAGTGCCTCCGCTGACCATGACCTG
ACTGACAAGAGCATCAACTCTCTGGGTGACTTTGTCCCATAAGGTGAAGTGACCAGTGACTTTGTCATGCTGAAGGAATG
TGTGGTGGGAACCAAGAAGTGAGTGCTCACCCTTCACAAGTCTTTGCTGGCTCAGACCAAATGGTGGGCTCTGGAGAAGA
CTGACCTTAAATTTATTGACACCACTGCCAAGTTTGGCCATGGCTGCTCCCAGACCATGTAAGAAAGAAAATATTCATGG
AAAGTATTCATGAAACCACTCAAGAAAGACCAAATTGCAATAGAAGATGGAGCT

Alignment

ORF - retro_mmul_973 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.44 %
• Parental protein coverage: 87.75 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PRGLRTFKTVFAEHISDECKRRFYKNWHKSKKKAFTKYCKKWQDEDGKKQLEKDFSSMKKYCQVIRVIAH
          P.GL.T.KT.FA.HIS.ECK..F.KN.HKSKKKAFT.YCKKWQ..D.KKQLE.DFSSMKKYCQVI.V.AH
Retrocopy PQGLQTSKTIFAKHISNECKKHFSKN*HKSKKKAFTSYCKKWQNKDSKKQLEQDFSSMKKYCQVIHVTAH

Parental  TQMRLLPLRQKKAHLMEIQVNGGTVAEKLDWARERLEQQVPVNQVFGQDEMIDVIGVTKGKGYKGVTSRW
          T.M.LLP.RQKKA.LMEIQVN.GTVA.KLDW.RERLEQQVPVNQVFGQDEMID...VTKGK.YKGVTS.W
Retrocopy THMHLLPVRQKKAPLMEIQVNRGTVAKKLDWDRERLEQQVPVNQVFGQDEMIDIFKVTKGKDYKGVTSHW

Parental  HTKKLPRKTHRGLRKVACIGAWHPARV-AFSVARAGQKGYHHRTEINKKIYKIGQGYLIKDGKLIKNNAS
          H.KKLP.KT..GL.KVA.IGAWHPA.V..FSVA..GQKGYHH.T.....I...GQGYLIKD.KLIKN.AS
Retrocopy HAKKLPCKTQ*GLCKVAWIGAWHPACV>TFSVACTGQKGYHHHT-TRRSICMTGQGYLIKDDKLIKNSAS

Parental  TDYDLSDKSINPLGGFVHYGEVTNDFVMLKGCVVGTKKRVLTLRKSLLVQTKRRALEKIDLKFIDTTSKF
          .D.DL.DKSIN.LG.FV..GEVT.DFVMLK.CVVGTKK.VLTL.KSLL.QTK..ALEK.DLKFIDTT.KF
Retrocopy ADHDLTDKSINSLGDFVP*GEVTSDFVMLKECVVGTKK*VLTLHKSLLAQTKWWALEKTDLKFIDTTAKF

Parental  GHGRFQTMEEKK----AFMGPLKKDRIAKEEGA
          GHG..QTM.E.K.....FM.PLKKD.IA.E.GA
Retrocopy GHGCSQTM*ERKYSWKVFMKPLKKDQIAIEDGA

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	0.22 RPM	88.41 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	471.22 RPM
SRP007412_cerebellum	0.13 RPM	130.96 RPM
SRP007412_heart	0.00 RPM	122.84 RPM
SRP007412_kidney	0.00 RPM	153.87 RPM
SRP007412_liver	0.00 RPM	264.62 RPM
SRP007412_testis	0.11 RPM	165.21 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_973 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_973 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_973 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2403
Pan troglodytes	retro_ptro_1753
Gorilla gorilla	retro_ggor_1822
Pongo abelii	retro_pabe_2167

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 110 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010853	1 retrocopy	retro_amel_1115,
Bos taurus	ENSBTAG00000003228	3 retrocopies	retro_btau_1644, retro_btau_281, retro_btau_341,
Canis familiaris	ENSCAFG00000001346	1 retrocopy	retro_cfam_97,
Dasypus novemcinctus	ENSDNOG00000001121	4 retrocopies	retro_dnov_1359, retro_dnov_1641, retro_dnov_652, retro_dnov_788,
Equus caballus	ENSECAG00000020665	1 retrocopy	retro_ecab_897,
Erinaceus europaeus	ENSEEUG00000014661	2 retrocopies	retro_eeur_488, retro_eeur_557,
Echinops telfairi	ENSETEG00000011380	5 retrocopies	retro_etel_1646, retro_etel_2199, retro_etel_2212, retro_etel_657, retro_etel_972,
Felis catus	ENSFCAG00000005820	1 retrocopy	retro_fcat_1809,
Macropus eugenii	ENSMEUG00000009789	26 retrocopies	retro_meug_1045, retro_meug_118, retro_meug_1210, retro_meug_1403, retro_meug_1452, retro_meug_1492, retro_meug_1516, retro_meug_1554, retro_meug_1589, retro_meug_1604, retro_meug_1698, retro_meug_1856, retro_meug_2150, retro_meug_2151, retro_meug_221, retro_meug_367, retro_meug_412, retro_meug_461, retro_meug_592, retro_meug_677, retro_meug_683, retro_meug_831, retro_meug_851, retro_meug_886, retro_meug_889, retro_meug_898,
Myotis lucifugus	ENSMLUG00000023711	1 retrocopy	retro_mluc_810,
Macaca mulatta	ENSMMUG00000010029	4 retrocopies	retro_mmul_1170, retro_mmul_149, retro_mmul_2334, retro_mmul_973 ,
Monodelphis domestica	ENSMODG00000009539	2 retrocopies	retro_mdom_380, retro_mdom_408,
Mustela putorius furo	ENSMPUG00000013271	3 retrocopies	retro_mputfur_1284, retro_mputfur_199, retro_mputfur_774,
Mus musculus	ENSMUSG00000060036	30 retrocopies	retro_mmus_1148, retro_mmus_1158, retro_mmus_1164, retro_mmus_1165, retro_mmus_1167, retro_mmus_1183, retro_mmus_1238, retro_mmus_1239, retro_mmus_1240, retro_mmus_1241, retro_mmus_1242, retro_mmus_1243, retro_mmus_1244, retro_mmus_1245, retro_mmus_1246, retro_mmus_1465, retro_mmus_1548, retro_mmus_2231, retro_mmus_2275, retro_mmus_2276, retro_mmus_2474, retro_mmus_2501, retro_mmus_2547, retro_mmus_2849, retro_mmus_3125, retro_mmus_3215, retro_mmus_3422, retro_mmus_3467, retro_mmus_361, retro_mmus_897,
Nomascus leucogenys	ENSNLEG00000015234	2 retrocopies	retro_nleu_1038, retro_nleu_1449,
Oryctolagus cuniculus	ENSOCUG00000027712	4 retrocopies	retro_ocun_105, retro_ocun_179, retro_ocun_1893, retro_ocun_558,
Otolemur garnettii	ENSOGAG00000000032	7 retrocopies	retro_ogar_1264, retro_ogar_1679, retro_ogar_2096, retro_ogar_2122, retro_ogar_2448, retro_ogar_3431, retro_ogar_960,
Ochotona princeps	ENSOPRG00000013088	3 retrocopies	retro_opri_1004, retro_opri_1014, retro_opri_432,
Procavia capensis	ENSPCAG00000010642	1 retrocopy	retro_pcap_115,
Pteropus vampyrus	ENSPVAG00000003204	2 retrocopies	retro_pvam_1220, retro_pvam_1390,
Rattus norvegicus	ENSRNOG00000016896	2 retrocopies	retro_rnor_1333, retro_rnor_731,
Sarcophilus harrisii	ENSSHAG00000003212	2 retrocopies	retro_shar_154, retro_shar_662,
Tupaia belangeri	ENSTBEG00000005989	1 retrocopy	retro_tbel_939,
Tursiops truncatus	ENSTTRG00000010880	2 retrocopies	retro_ttru_1266, retro_ttru_1518,