RetrogeneDB ID: retro_mmul_676

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1099214323025:1126..1460(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL26L1
• Ensembl ID: ENSMMUG00000003070
• Aliases: None
• Description: ribosomal protein L26-like 1 [Source:RefSeq peptide;Acc:NP_001253942]

Sequence

>retro_mmul_676
AGCAAGGAGCTGCAGCAGAAGCACAGTGTCCACTCCACGCCCATCCACAAGGATAAAAAGATCCAGGTGGTTGGAAGACA
CTGCAAAGGTTAGCAAATCAGCAAGCTGGTCCAGATGTACATAAGGAAATATATCATCTACATGGAGCAGGTGCAGTGCG
AAAAGAGCCAATGGCACTGCCGTCTATGTGGGCATTTGCCCGAGCCAGGTGGTGATCACCAGGCTAAAGCTGGACCAGAA
ATGGGAAAAAGTTCTTGAATGCAAAGCTGAGTCTCAACAAGTCAGAAAAGGGAAAGGCAAATATAAGGAAGAGCTTACTG
AGAAAATGCAGGAA

Alignment

ORF - retro_mmul_676 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.07 %
• Parental protein coverage: 76.55 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SKELRQKYNVRSMPIRKDDEVQVVRGHYKGQQIGKVVQVYRKKYVIYIERVQREK-ANGTTVHVGIHPSK
          SKEL.QK..V.S.PI.KD...QVV..H.KG.QI.K.VQ.Y..KY.IY.E.VQ.EK.ANGT.V.VGI.PS.
Retrocopy SKELQQKHSVHSTPIHKDKKIQVVGRHCKG*QISKLVQMYIRKYIIYMEQVQCEK>ANGTAVYVGICPSQ

Parental  VVITRLKLDKDRKKILERKAKSRQVGKEKGKYKEELIEKMQE
          VVITRLKLD....K.LE.KA.S.QV.K.KGKYKEEL.EKMQE
Retrocopy VVITRLKLDQKWEKVLECKAESQQVRKGKGKYKEELTEKMQE

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	20.39 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	27.84 RPM
SRP007412_cerebellum	0.00 RPM	17.37 RPM
SRP007412_heart	0.00 RPM	17.49 RPM
SRP007412_kidney	0.00 RPM	19.48 RPM
SRP007412_liver	0.00 RPM	22.48 RPM
SRP007412_testis	0.00 RPM	80.70 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_676 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_676 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_676 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 107 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000002289	35 retrocopies	retro_dnov_1106, retro_dnov_1147, retro_dnov_1171, retro_dnov_1258, retro_dnov_1304, retro_dnov_1319, retro_dnov_1344, retro_dnov_1381, retro_dnov_1501, retro_dnov_1676, retro_dnov_1819, retro_dnov_1959, retro_dnov_2039, retro_dnov_2041, retro_dnov_2061, retro_dnov_2078, retro_dnov_2103, retro_dnov_2116, retro_dnov_2121, retro_dnov_2287, retro_dnov_2297, retro_dnov_2438, retro_dnov_2545, retro_dnov_2580, retro_dnov_2632, retro_dnov_300, retro_dnov_306, retro_dnov_467, retro_dnov_646, retro_dnov_666, retro_dnov_681, retro_dnov_760, retro_dnov_850, retro_dnov_970, retro_dnov_985,
Felis catus	ENSFCAG00000026949	1 retrocopy	retro_fcat_524,
Homo sapiens	ENSG00000037241	2 retrocopies	retro_hsap_586, retro_hsap_837,
Latimeria chalumnae	ENSLACG00000007599	2 retrocopies	retro_lcha_5, retro_lcha_8,
Microcebus murinus	ENSMICG00000011312	10 retrocopies	retro_mmur_1020, retro_mmur_1144, retro_mmur_313, retro_mmur_327, retro_mmur_346, retro_mmur_412, retro_mmur_471, retro_mmur_623, retro_mmur_72, retro_mmur_75,
Macaca mulatta	ENSMMUG00000003070	1 retrocopy	retro_mmul_676 ,
Macaca mulatta	ENSMMUG00000003448	22 retrocopies	retro_mmul_1117, retro_mmul_1361, retro_mmul_1398, retro_mmul_1497, retro_mmul_1710, retro_mmul_1773, retro_mmul_1899, retro_mmul_1986, retro_mmul_2052, retro_mmul_2163, retro_mmul_2332, retro_mmul_2344, retro_mmul_325, retro_mmul_360, retro_mmul_398, retro_mmul_405, retro_mmul_448, retro_mmul_548, retro_mmul_805, retro_mmul_903, retro_mmul_920, retro_mmul_992,
Oryctolagus cuniculus	ENSOCUG00000006172	4 retrocopies	retro_ocun_1015, retro_ocun_1224, retro_ocun_354, retro_ocun_845,
Procavia capensis	ENSPCAG00000002246	10 retrocopies	retro_pcap_137, retro_pcap_157, retro_pcap_188, retro_pcap_204, retro_pcap_337, retro_pcap_404, retro_pcap_419, retro_pcap_42, retro_pcap_422, retro_pcap_448,
Pteropus vampyrus	ENSPVAG00000003253	8 retrocopies	retro_pvam_1062, retro_pvam_1208, retro_pvam_122, retro_pvam_353, retro_pvam_688, retro_pvam_71, retro_pvam_769, retro_pvam_877,
Sus scrofa	ENSSSCG00000016989	3 retrocopies	retro_sscr_1104, retro_sscr_462, retro_sscr_685,
Ictidomys tridecemlineatus	ENSSTOG00000026876	1 retrocopy	retro_itri_1141,
Tursiops truncatus	ENSTTRG00000010624	8 retrocopies	retro_ttru_1070, retro_ttru_1124, retro_ttru_1694, retro_ttru_1818, retro_ttru_364, retro_ttru_386, retro_ttru_474, retro_ttru_646,