RetrogeneDB ID: retro_mmul_2047

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 6:148292910..148293850(+)
• Located in intron of: ENSMMUG00000014704

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.345
• Ensembl ID: ENSMMUG00000022884
• Aliases: None
• Description: glutamine synthetase [Source:RefSeq peptide;Acc:NP_001252942]

Sequence

>retro_mmul_2047
TGGCATTTTGATGGCTGTAGTATTTTACAGTCTGAAGGCGCCAACAGTGACATGCATTTCGTGCCTGCTGCCATGTTTTG
GGATACCTTCAGTAAAGACCCTACAAGCTGGTGTTCTGTGAAGTTTTCAAGTACAACCAAAAGGCTGCAGAGACCAATTT
GAGGCACACCTGTAAGTGGATAATGGACATGGTGAGCAACCACTTCCCCTGGTTTGGCATGGACCAGGAATATCCCCTCA
TGGGGACAGATGGGCACCCCTTTGGTTGGCCTTCCAATGGCTTCCCAGGACCCCAGGTCCATATTACTGCAGTGTGGGAG
CAGACAAAGCCTATGGCACAGACATTGTGGAGGCCCATTACCAGGCCTGCTTGTATGCTGGAGTCAAGATGGCAGGGACT
AATGCTGAGGTCACGCCTGCCCAGTGGGAATTTCTAATCGGATGCTGTGAAGGAATCAGCATGGGAGATCATTTCTGAGT
GGCCTGTTTCATTTTGCATCATGTATGTGAAGACTTTGGAGTGATAGCAACCTTTGATCCTAAGCCCATTCCTGGGAACT
GGAAGGGTACAGGCTGCCATACCAACTTTAGCACCAAGGCCATGTGGGAGGAGAATAGTCTGAAGTACATTGAGTAGGCC
ATCGAGAAACTAAGCAAGTGGCACTAGTACCACATCCGTTCCTATGATCCCAAGGGAGGCCTGGACAAAGCCCAGCACGT
AGCTGGATTCCACAAAACCTCCAACATCAACGACTTTTCTGCTGGTGTAGCCAATTGTAGTGCCAACATATGCATTCCCT
GGACTGTTGGCCAGGAGAAGAAGGGTTACTTTGAAGACCGTCGCCACTCTGCCAACTGCGAACCCTTTTCGGTGACAGAA
GCCCTCATCCACATGTGTCTTCCCAATGAAACCGGCAGTGAGCTCTTCCAGTACAAAAAC

Alignment

ORF - retro_mmul_2047 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.65 %
• Parental protein coverage: 84.18 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  WNFDGSSTLQSEGSNSDMYLVPAAMFRDPFRKDPN-KLVLCEVFKYNRRPAETNLRHTCKRIMDMVSNQH
          W.FDG.S.LQSEG.NSDM..VPAAMF.D.F.KDP..KLV.CEVFKYN...AETNLRHTCK.IMDMVSN..
Retrocopy WHFDGCSILQSEGANSDMHFVPAAMFWDTFSKDPT<KLVFCEVFKYNQKAAETNLRHTCKWIMDMVSNHF

Parental  PWFGMEQEYTLMGTDGHPFGWPSNGFPGPQ-GPYYCGVGADRAYGRDIVEAHYRACLYAGVKIAGTNAEV
          PWFGM.QEY.LMGTDGHPFGWPSNGFPGPQ.GPYYC.VGAD.AYG.DIVEAHY.ACLYAGVK.AGTNAEV
Retrocopy PWFGMDQEYPLMGTDGHPFGWPSNGFPGPQ<GPYYCSVGADKAYGTDIVEAHYQACLYAGVKMAGTNAEV

Parental  MPAQWEFQIGPCEGISMGDHLWVARFILHRVCEDFGVIATFDPKPIPGNWNGAGCHTNFSTKAMREENGL
          .PAQWEF.IG.CEGISMGDH..VA.FILH.VCEDFGVIATFDPKPIPGNW.G.GCHTNFSTKAM.EEN.L
Retrocopy TPAQWEFLIGCCEGISMGDHF*VACFILHHVCEDFGVIATFDPKPIPGNWKGTGCHTNFSTKAMWEENSL

Parental  KYIEEAIEKLSKRHQYHIRAYDPKGGLDNARRLTGFHETSNINDFSAGVANRSASIRIPRTVGQEKKGYF
          KYIE.AIEKLSK.H.YHIR.YDPKGGLD.A....GFH.TSNINDFSAGVAN.SA.I.IP.TVGQEKKGYF
Retrocopy KYIE*AIEKLSKWH*YHIRSYDPKGGLDKAQHVAGFHKTSNINDFSAGVANCSANICIPWTVGQEKKGYF

Parental  EDRRPSANCDPFSVTEALIRTCLLNETGDEPFQYKN
          EDRR.SANC.PFSVTEALI..CL.NETG.E.FQYKN
Retrocopy EDRRHSANCEPFSVTEALIHMCLPNETGSELFQYKN

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	598.24 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	850.10 RPM
SRP007412_cerebellum	0.13 RPM	345.93 RPM
SRP007412_heart	0.00 RPM	212.40 RPM
SRP007412_kidney	0.12 RPM	71.48 RPM
SRP007412_liver	0.00 RPM	177.22 RPM
SRP007412_testis	0.15 RPM	1206.94 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2047 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2047 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2047 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3255
Pan troglodytes	retro_ptro_2201
Gorilla gorilla	retro_ggor_2216
Pongo abelii	retro_pabe_2698

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 57 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013631	4 retrocopies	retro_btau_1050, retro_btau_1474, retro_btau_336, retro_btau_824,
Canis familiaris	ENSCAFG00000013102	2 retrocopies	retro_cfam_1691, retro_cfam_2143,
Callithrix jacchus	ENSCJAG00000004654	1 retrocopy	retro_cjac_2837,
Dasypus novemcinctus	ENSDNOG00000013948	4 retrocopies	retro_dnov_1386, retro_dnov_1870, retro_dnov_2393, retro_dnov_842,
Equus caballus	ENSECAG00000015865	1 retrocopy	retro_ecab_979,
Echinops telfairi	ENSETEG00000008329	3 retrocopies	retro_etel_143, retro_etel_189, retro_etel_1968,
Felis catus	ENSFCAG00000010551	1 retrocopy	retro_fcat_1811,
Homo sapiens	ENSG00000135821	4 retrocopies	retro_hsap_2364, retro_hsap_3255, retro_hsap_848, retro_hsap_935,
Gorilla gorilla	ENSGGOG00000024712	3 retrocopies	retro_ggor_1794, retro_ggor_2216, retro_ggor_754,
Loxodonta africana	ENSLAFG00000000700	1 retrocopy	retro_lafr_196,
Macropus eugenii	ENSMEUG00000001774	6 retrocopies	retro_meug_1013, retro_meug_1394, retro_meug_1561, retro_meug_409, retro_meug_433, retro_meug_746,
Macaca mulatta	ENSMMUG00000022884	2 retrocopies	retro_mmul_2047 , retro_mmul_954,
Monodelphis domestica	ENSMODG00000006787	4 retrocopies	retro_mdom_1268, retro_mdom_488, retro_mdom_823, retro_mdom_892,
Mus musculus	ENSMUSG00000026473	3 retrocopies	retro_mmus_1730, retro_mmus_1767, retro_mmus_696,
Nomascus leucogenys	ENSNLEG00000018007	3 retrocopies	retro_nleu_1388, retro_nleu_293, retro_nleu_416,
Pongo abelii	ENSPPYG00000000440	1 retrocopy	retro_pabe_2698,
Pan troglodytes	ENSPTRG00000001751	4 retrocopies	retro_ptro_2201, retro_ptro_2823, retro_ptro_589, retro_ptro_647,
Sarcophilus harrisii	ENSSHAG00000000116	1 retrocopy	retro_shar_553,
Sus scrofa	ENSSSCG00000015545	1 retrocopy	retro_sscr_726,
Ictidomys tridecemlineatus	ENSSTOG00000014529	2 retrocopies	retro_itri_1083, retro_itri_743,
Tupaia belangeri	ENSTBEG00000003522	3 retrocopies	retro_tbel_2230, retro_tbel_3079, retro_tbel_3992,
Tarsius syrichta	ENSTSYG00000002066	1 retrocopy	retro_tsyr_385,
Tursiops truncatus	ENSTTRG00000010781	1 retrocopy	retro_ttru_543,
Drosophila melanogaster	FBgn0001145	1 retrocopy	retro_dmel_44,