RetrogeneDB ID: retro_mmul_588

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:221578509..221578719(-)
• Located in intron of: ENSMMUG00000008426

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.17369
• Ensembl ID: ENSMMUG00000005006
• Aliases: None
• Description: 40S ribosomal protein S21 [Source:UniProtKB/TrEMBL;Acc:F7AM79]

Sequence

>retro_mmul_588
ATGCAGAAAGATGCCAGCAAGTTCGTGGACCTGTGCATGGGGCAGAAATGCTCCACCAGCAACTGCGTCATCAGTGCCAA
GGACCATATATCCATGTGGATGAATGTGGCCAAGGCCAACAAGGTCACGGGCAGGTTTAACAGCTAGTTTAAAACCTGTG
CTATCTGCAGGACAGTTTGCAGGATGGGTGAGTCAGATGATTCCATTCTC

Alignment

ORF - retro_mmul_588 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.71 %
• Parental protein coverage: 84.34 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MQNDAGEFVDLYVPRKCSASNRIIGAKDHASIQMNVAEVDKVTGRFNGQFKTYAICGAIRRMGESDDSIL
          MQ.DA..FVDL....KCS.SN..I.AKDH.S..MNVA...KVTGRFN..FKT.AIC....RMGESDDSIL
Retrocopy MQKDASKFVDLCMGQKCSTSNCVISAKDHISMWMNVAKANKVTGRFNS*FKTCAICRTVCRMGESDDSIL

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	35.30 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	149.85 RPM
SRP007412_cerebellum	0.00 RPM	33.06 RPM
SRP007412_heart	0.00 RPM	62.30 RPM
SRP007412_kidney	0.00 RPM	49.76 RPM
SRP007412_liver	0.04 RPM	228.60 RPM
SRP007412_testis	0.04 RPM	37.81 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_588 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_588 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_588 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_365

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 73 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017399	2 retrocopies	retro_amel_1783, retro_amel_87,
Bos taurus	ENSBTAG00000020795	2 retrocopies	retro_btau_174, retro_btau_1780,
Canis familiaris	ENSCAFG00000012676	4 retrocopies	retro_cfam_1055, retro_cfam_1687, retro_cfam_1896, retro_cfam_28,
Callithrix jacchus	ENSCJAG00000014195	5 retrocopies	retro_cjac_2266, retro_cjac_2572, retro_cjac_629, retro_cjac_82, retro_cjac_884,
Erinaceus europaeus	ENSEEUG00000004573	2 retrocopies	retro_eeur_235, retro_eeur_501,
Gorilla gorilla	ENSGGOG00000023745	7 retrocopies	retro_ggor_131, retro_ggor_1380, retro_ggor_1647, retro_ggor_2043, retro_ggor_2089, retro_ggor_2875, retro_ggor_917,
Latimeria chalumnae	ENSLACG00000012753	1 retrocopy	retro_lcha_124,
Loxodonta africana	ENSLAFG00000015793	4 retrocopies	retro_lafr_1055, retro_lafr_1237, retro_lafr_352, retro_lafr_499,
Macropus eugenii	ENSMEUG00000015832	2 retrocopies	retro_meug_1221, retro_meug_466,
Microcebus murinus	ENSMICG00000012997	5 retrocopies	retro_mmur_110, retro_mmur_1388, retro_mmur_264, retro_mmur_55, retro_mmur_965,
Macaca mulatta	ENSMMUG00000005006	8 retrocopies	retro_mmul_1006, retro_mmul_1043, retro_mmul_1138, retro_mmul_1279, retro_mmul_1331, retro_mmul_1948, retro_mmul_588 , retro_mmul_633,
Ochotona princeps	ENSOPRG00000000937	1 retrocopy	retro_opri_996,
Pongo abelii	ENSPPYG00000011205	8 retrocopies	retro_pabe_1562, retro_pabe_157, retro_pabe_2446, retro_pabe_2505, retro_pabe_3503, retro_pabe_365, retro_pabe_710, retro_pabe_986,
Pan troglodytes	ENSPTRG00000013708	1 retrocopy	retro_ptro_42,
Pteropus vampyrus	ENSPVAG00000003548	2 retrocopies	retro_pvam_1362, retro_pvam_1368,
Rattus norvegicus	ENSRNOG00000006325	2 retrocopies	retro_rnor_128, retro_rnor_172,
Sus scrofa	ENSSSCG00000021825	1 retrocopy	retro_sscr_7,
Ictidomys tridecemlineatus	ENSSTOG00000001029	5 retrocopies	retro_itri_1027, retro_itri_1487, retro_itri_637, retro_itri_82, retro_itri_849,
Tarsius syrichta	ENSTSYG00000007061	5 retrocopies	retro_tsyr_105, retro_tsyr_123, retro_tsyr_1502, retro_tsyr_2157, retro_tsyr_951,
Tursiops truncatus	ENSTTRG00000011105	6 retrocopies	retro_ttru_1058, retro_ttru_1418, retro_ttru_1707, retro_ttru_1749, retro_ttru_1773, retro_ttru_674,