RetrogeneDB ID: retro_mmul_1870

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 5:8777333..8777846(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.9732
• Ensembl ID: ENSMMUG00000003795
• Aliases: None
• Description: None

Sequence

>retro_mmul_1870
ATGCTGGTCACCAGGAAGACTTTCTGTTGGCACTGGGATGACTCAGAGTCAGAGGAAGATGAGGAGGACTCAGAGGAGGT
TCAATTAAAACTGGAATAGACTAGATAAGTACATAATATAAGGAAGAGATTCAATGGGTGCTGTGGCCCTGCTGTTGGGA
AAGAAGGTACAAGAAGAGATCACTCAGATCCCTTTCAGATGAAGACAGGTGATGTGGTGGATATGAAGAAATGGAAGGAA
AAGGGCAAAGATAAAATCAGTAAAGAGGAAGACTTTCACTTGGGGACATCATTTTCTGCAGAAACCAACTGAAGGGATGA
GGATGCAGACATGATGAAGTACACTGAGACAGAGCTAAAGAAGAAAGGGATCGTGGAACATGAGGAACAGAAAGTCAAGC
CAAGGAATGCAGAGGATTGTCTTTATGAACTTCCAGAAAACCTCCACATTTCCTCAGCAAAGAAGACCAAGAAGATATTT
TCCAACCAGATGCTGAATGGCATTCCTGAGTTG

Alignment

ORF - retro_mmul_1870 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.03 %
• Parental protein coverage: 60.9 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPVVRKIFRRRRGDSESEEDEQDSEEVRLKLEETREVQNLRKRPNGVSAVALLVGE-KVQEETTLVDDPF
          M.V.RK.F.....DSESEEDE.DSEEV.LKLE.TR.V.N.RKR.NG....A..VG..KVQEE.T....PF
Retrocopy MLVTRKTFCWHWDDSESEEDEEDSEEVQLKLE*TR*VHNIRKRFNGCCGPA--VGK>KVQEEITQI--PF

Parental  -QMKTGGMVDMKKLKERGKDKISEEEDLHLGTSFSAETNRRDEDADMMKYIETELKKRKGIVEHEEQKVK
          .QMKTG..VDMKK.KE.GKDKIS.EED.HLGTSFSAETN.RDEDADMMKY.ETELKK.KGIVEHEEQKVK
Retrocopy <QMKTGDVVDMKKWKEKGKDKISKEEDFHLGTSFSAETN*RDEDADMMKYTETELKK-KGIVEHEEQKVK

Parental  PKNAEDCLYELPENIRVSSAKKTEEMLSNQMLSGIPEV
          P.NAEDCLYELPEN...SSAKKT....SNQML.GIPE.
Retrocopy PRNAEDCLYELPENLHISSAKKTKKIFSNQMLNGIPEL

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	55.69 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	57.91 RPM
SRP007412_cerebellum	0.00 RPM	43.52 RPM
SRP007412_heart	0.00 RPM	37.16 RPM
SRP007412_kidney	0.00 RPM	34.51 RPM
SRP007412_liver	0.00 RPM	17.22 RPM
SRP007412_testis	0.00 RPM	75.76 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1870 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1870 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1870 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2913
Pan troglodytes	retro_ptro_1969
Pongo abelii	retro_pabe_2426
Callithrix jacchus	retro_cjac_2299

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000019979	1 retrocopy	retro_cfam_116,
Choloepus hoffmanni	ENSCHOG00000013895	3 retrocopies	retro_chof_1103, retro_chof_1747, retro_chof_978,
Callithrix jacchus	ENSCJAG00000020318	3 retrocopies	retro_cjac_1757, retro_cjac_2299, retro_cjac_2778,
Dasypus novemcinctus	ENSDNOG00000019214	1 retrocopy	retro_dnov_1540,
Homo sapiens	ENSG00000136819	3 retrocopies	retro_hsap_2872, retro_hsap_2913, retro_hsap_320,
Gorilla gorilla	ENSGGOG00000013358	1 retrocopy	retro_ggor_1990,
Macropus eugenii	ENSMEUG00000010524	3 retrocopies	retro_meug_1046, retro_meug_1241, retro_meug_508,
Macaca mulatta	ENSMMUG00000003795	2 retrocopies	retro_mmul_1460, retro_mmul_1870 ,
Monodelphis domestica	ENSMODG00000006832	1 retrocopy	retro_mdom_518,
Nomascus leucogenys	ENSNLEG00000017658	3 retrocopies	retro_nleu_1763, retro_nleu_614, retro_nleu_823,
Otolemur garnettii	ENSOGAG00000009770	1 retrocopy	retro_ogar_1015,
Pongo abelii	ENSPPYG00000019685	1 retrocopy	retro_pabe_2426,
Pan troglodytes	ENSPTRG00000021465	3 retrocopies	retro_ptro_1943, retro_ptro_1969, retro_ptro_258,
Sarcophilus harrisii	ENSSHAG00000012313	1 retrocopy	retro_shar_746,