RetrogeneDB ID: retro_mmul_923

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 12:65996456..65997004(+)
• Located in intron of: ENSMMUG00000001883

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.710
• Ensembl ID: ENSMMUG00000022451
• Aliases: None
• Description: proteasome subunit alpha type-2 [Source:RefSeq peptide;Acc:NP_001253810]

Sequence

>retro_mmul_923
ATAGCAACCGAGAAAAAACAGAAATTCATTCTGTATGATGAGCGAAGTGTACACAAAGTGGGACCAATTATCAAGCATAC
AGGTTTGGTGTACAGTGGCGTGGACCGAGATGTGCACAGAGCTCAAAACTAGCTCAACAATACTATCTTGTGTACCAAGT
GCCCATTCCCACAGCTCACCTAGTACAGAGAGTGGCTTCTGTGATATAAGAATGTACTCAGTCAGGTGGTGTTCGTTCAT
TTGGAGTTTCTTTACTTGTTTGTGGTTGGAATAAGGGACGACCATATTTATTTCAGTCAGATCCATCTGGAGCTTACTTG
GCATGGAAAGCCACAGCAATGGGAAAGAACTATGTGAATGGGAAAACTTCCCTTGAGAAAAAATAAAATGAAGATCTGGA
ACTTGAAGATGCCATTCATACAGCCGTCTTAACCCTAAAGGAAAACTTTGAAGGCCAAATGACAGAGGATAATATAGAAG
GTGGAATCTTCAACGATGCTGGATTTAGGGGGCTTACTCCAACTGAAGTTAAGAATTACTTGGCTGCC

Alignment

ORF - retro_mmul_923 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.45 %
• Parental protein coverage: 79.91 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LATEKKQKSILYDERSVHKVEPITKHIGLVYSGMGPDYRVLVHRAR-KLAQQYYLVYQEPIPTAQLVQRV
          .ATEKKQK.ILYDERSVHKV.PI.KH.GLVYSG...D....VHRA..KLAQQYYLVYQ.PIPTA.LVQRV
Retrocopy IATEKKQKFILYDERSVHKVGPIIKHTGLVYSGVDRD----VHRAQ<KLAQQYYLVYQVPIPTAHLVQRV

Parental  ASVMQEYTQSGGVRPFGVSLLICGWNEGRPYLFQSDPSGAYFAWKATAMGKNYVNGKTFLEKRYNEDLEL
          ASV..E.TQSGGVR.FGVSLL.CGWN.GRPYLFQSDPSGAY.AWKATAMGKNYVNGKT.LEK..NEDLEL
Retrocopy ASVI*ECTQSGGVRSFGVSLLVCGWNKGRPYLFQSDPSGAYLAWKATAMGKNYVNGKTSLEKK*NEDLEL

Parental  EDAIHTAILTLKESFEGQMTEDNIEVGICNEAGFRRLTPTEVKDYLAA
          EDAIHTA.LTLKE.FEGQMTEDNIE.GI.N.AGFR.LTPTEVK.YLAA
Retrocopy EDAIHTAVLTLKENFEGQMTEDNIEGGIFNDAGFRGLTPTEVKNYLAA

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	29.81 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	25.78 RPM
SRP007412_cerebellum	0.06 RPM	36.29 RPM
SRP007412_heart	0.00 RPM	36.27 RPM
SRP007412_kidney	0.12 RPM	50.82 RPM
SRP007412_liver	0.04 RPM	38.52 RPM
SRP007412_testis	0.30 RPM	36.30 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_923 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_923 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_923 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2199
Pan troglodytes	retro_ptro_1670
Pongo abelii	retro_pabe_2076

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000000990	3 retrocopies	retro_btau_296, retro_btau_384, retro_btau_889,
Choloepus hoffmanni	ENSCHOG00000000644	1 retrocopy	retro_chof_893,
Callithrix jacchus	ENSCJAG00000007730	4 retrocopies	retro_cjac_1096, retro_cjac_1868, retro_cjac_2583, retro_cjac_852,
Cavia porcellus	ENSCPOG00000013134	1 retrocopy	retro_cpor_1512,
Dasypus novemcinctus	ENSDNOG00000011910	2 retrocopies	retro_dnov_2202, retro_dnov_724,
Echinops telfairi	ENSETEG00000015835	2 retrocopies	retro_etel_1569, retro_etel_2022,
Homo sapiens	ENSG00000106588	2 retrocopies	retro_hsap_2199, retro_hsap_908,
Gorilla gorilla	ENSGGOG00000006538	1 retrocopy	retro_ggor_735,
Myotis lucifugus	ENSMLUG00000010086	2 retrocopies	retro_mluc_1050, retro_mluc_135,
Macaca mulatta	ENSMMUG00000022451	2 retrocopies	retro_mmul_1114, retro_mmul_923 ,
Nomascus leucogenys	ENSNLEG00000003177	1 retrocopy	retro_nleu_329,
Oryctolagus cuniculus	ENSOCUG00000012092	1 retrocopy	retro_ocun_774,
Ochotona princeps	ENSOPRG00000011793	2 retrocopies	retro_opri_135, retro_opri_791,
Pongo abelii	ENSPPYG00000017612	2 retrocopies	retro_pabe_2076, retro_pabe_783,
Pan troglodytes	ENSPTRG00000019120	2 retrocopies	retro_ptro_1670, retro_ptro_628,
Ictidomys tridecemlineatus	ENSSTOG00000013334	1 retrocopy	retro_itri_223,
Tarsius syrichta	ENSTSYG00000014299	2 retrocopies	retro_tsyr_132, retro_tsyr_246,
Tursiops truncatus	ENSTTRG00000005649	1 retrocopy	retro_ttru_356,