RetrogeneDB ID: retro_mmul_1563

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 20:49325490..49325947(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SOD1
• Ensembl ID: ENSMMUG00000001711
• Aliases: None
• Description: Superoxide dismutase [Cu-Zn] [Source:UniProtKB/Swiss-Prot;Acc:Q8HXQ0]

Sequence

>retro_mmul_1563
CTAATGATAAAGGTCATGTGCACGTTGAAGGGCCAGAGCCCAGTACAGGGCACCATCCACTTTGGGCAGAAGGAAAATGG
ACCATTTTTGGTGTCAGAATGCATTACAGGATTGACTGAATGCCAGCACAGACTTCGTGTTCATCAGTTTGGAGATAATA
CACCAGGCTGTACCAGGGCAGGTCCTTACTTTAATCCTTTAAACAAAAACCACAGTGGGCCAAGGATCAAGAGAGGCAGG
TTGGAGACTTGGGTAATGTGACCGCTGGCAAAGATGGGGTCACCAATGTATTTGTTGAAGATTCTCTGGTCTCATTCTCA
GGACACTATTCCATCACTGCCCACACAATGGTGTCCATGACAAACCAGATGACTTGGGCAAAGGTGAAAATGAAGAAAGT
ACAAACATGGGAAATGCTAGAAGTTGTTTGGCTTGTGGTTTAATTGGGATTGCCCAG

Alignment

ORF - retro_mmul_1563 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.38 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAMKAVCVLKGDSPVQGTINFEQKESNGPVKVWGSITGLTEGLHGFHVHQFGDNTQGCTSAGPHFNPLSR
          ...K..C.LKG.SPVQGTI.F.QKE.NGP..V...ITGLTE..H...VHQFGDNT.GCT.AGP.FNPL..
Retrocopy LMIKVMCTLKGQSPVQGTIHFGQKE-NGPFLVSECITGLTECQHRLRVHQFGDNTPGCTRAGPYFNPLNK

Parental  QHGGP-KDEERHVGDLGNVTAGKDGVAKVSFEDSVISLSGDHSIIGRTLV-VHEKADDLGKGGNEESKKT
          .H.GP.KD.ER.VGDLGNVTAGKDGV..V..EDS..S.SG..SI...T.V.VH.K.DDLGKG.NEES...
Retrocopy NHSGP<KDQERQVGDLGNVTAGKDGVTNVFVEDSLVSFSGHYSITAHTMV<VHDKPDDLGKGENEESTNM

Parental  GNAGGRLACGVIGIAQ
          GNA...LACG.IGIAQ
Retrocopy GNARSCLACGLIGIAQ

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	189.48 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	203.80 RPM
SRP007412_cerebellum	0.00 RPM	165.12 RPM
SRP007412_heart	0.00 RPM	165.53 RPM
SRP007412_kidney	0.00 RPM	340.96 RPM
SRP007412_liver	0.04 RPM	709.07 RPM
SRP007412_testis	0.00 RPM	61.25 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1563 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1563 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1563 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1637
Pan troglodytes	retro_ptro_1107
Gorilla gorilla	retro_ggor_1238
Pongo abelii	retro_pabe_1353
Callithrix jacchus	retro_cjac_1986

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Parental genes homology:

Parental genes homology involve 26 parental genes, and 65 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018854	1 retrocopy	retro_btau_40,
Canis familiaris	ENSCAFG00000008859	1 retrocopy	retro_cfam_1515,
Callithrix jacchus	ENSCJAG00000008983	3 retrocopies	retro_cjac_1477, retro_cjac_1986, retro_cjac_652,
Dasypus novemcinctus	ENSDNOG00000006512	1 retrocopy	retro_dnov_816,
Dipodomys ordii	ENSDORG00000013850	3 retrocopies	retro_dord_217, retro_dord_41, retro_dord_603,
Erinaceus europaeus	ENSEEUG00000015905	1 retrocopy	retro_eeur_305,
Felis catus	ENSFCAG00000002225	2 retrocopies	retro_fcat_1260, retro_fcat_422,
Homo sapiens	ENSG00000142168	3 retrocopies	retro_hsap_1637, retro_hsap_3591, retro_hsap_4117,
Gorilla gorilla	ENSGGOG00000015554	4 retrocopies	retro_ggor_1238, retro_ggor_2421, retro_ggor_2690, retro_ggor_2763,
Latimeria chalumnae	ENSLACG00000013736	1 retrocopy	retro_lcha_51,
Loxodonta africana	ENSLAFG00000010708	1 retrocopy	retro_lafr_127,
Microcebus murinus	ENSMICG00000005253	2 retrocopies	retro_mmur_378, retro_mmur_573,
Macaca mulatta	ENSMMUG00000001711	2 retrocopies	retro_mmul_1563 , retro_mmul_2372,
Monodelphis domestica	ENSMODG00000021041	1 retrocopy	retro_mdom_1376,
Mus musculus	ENSMUSG00000022982	1 retrocopy	retro_mmus_2742,
Nomascus leucogenys	ENSNLEG00000003545	3 retrocopies	retro_nleu_1324, retro_nleu_302, retro_nleu_584,
Otolemur garnettii	ENSOGAG00000014646	3 retrocopies	retro_ogar_27, retro_ogar_3364, retro_ogar_702,
Ochotona princeps	ENSOPRG00000007008	1 retrocopy	retro_opri_1190,
Pongo abelii	ENSPPYG00000011354	2 retrocopies	retro_pabe_1353, retro_pabe_3370,
Pan troglodytes	ENSPTRG00000013847	3 retrocopies	retro_ptro_1107, retro_ptro_2431, retro_ptro_2796,
Pteropus vampyrus	ENSPVAG00000005216	2 retrocopies	retro_pvam_281, retro_pvam_563,
Sarcophilus harrisii	ENSSHAG00000004195	1 retrocopy	retro_shar_278,
Ictidomys tridecemlineatus	ENSSTOG00000004434	1 retrocopy	retro_itri_1342,
Tupaia belangeri	ENSTBEG00000007333	4 retrocopies	retro_tbel_2131, retro_tbel_3531, retro_tbel_3611, retro_tbel_429,
Tarsius syrichta	ENSTSYG00000011342	17 retrocopies	retro_tsyr_1055, retro_tsyr_1064, retro_tsyr_1082, retro_tsyr_1112, retro_tsyr_1143, retro_tsyr_1176, retro_tsyr_1262, retro_tsyr_1275, retro_tsyr_1295, retro_tsyr_1369, retro_tsyr_1378, retro_tsyr_1590, retro_tsyr_2107, retro_tsyr_365, retro_tsyr_402, retro_tsyr_823, retro_tsyr_831,
Vicugna pacos	ENSVPAG00000012396	1 retrocopy	retro_vpac_168,