RetrogeneDB ID: retro_mmul_836

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 11:115510773..115511381(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.2014
• Ensembl ID: ENSMMUG00000010401
• Aliases: None
• Description: None

Sequence

>retro_mmul_836
GTGTCGAAGCTGCCACCCAAACCAGTCAAACCAGGGTAAGATAAAGTCGTCAGAGCCCTCTATACATTTGAACCCAGAAC
TCCAGATGAACTATGCTTTGAGGCAGGTGATATCATCTACATTACTGATATGAATGACGTCAGTTGGTGGAAAGGCACCT
CCAAAGGCAGGACTGGACTAACTCCAAGCAACTATGTGGCTGAGCAGGCAGAATCCATTGACAATCTATGTCTGAAGGAG
CAAAAAGAGGCAACTTGAGTTGGTTGCGAAGAGTGTTTGGACAACCGAGTGGGTGTTAATGGCTTAGACGAGGCTGGAAG
CACTGCCTTAGACTAGGTTTGTCATGGGATTTCAGAGATATAGTGGAAATGCTATTTACTCAACCGAGGATTTAACCGAG
CCAACAGAACAAGTTGGGAGACACAGCTTTGCATGCTGCTGCCTGGCAGGGTTATGCAGATATTGTCCAGTTGCTTCAGG
CAAAAGGTGTCAGAACAGGCTGAAGAAACAATGAGAAGAAGCTGGCTTTGGGCATGGTTAACAACGCCCATGGATCTCTC
CTGTAAAAGAAACAGGAGACAGATGCAGTTCGAACATTAAGCAATGCT

Alignment

ORF - retro_mmul_836 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.23 %
• Parental protein coverage: 95.33 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSKPPPKPVKPGQVKVFRALYTFEPRTPDELYFEEGDIIYITDMSDTNWWKGTSKGRTGLIPSNYVAEQA
          .SK.PPKPVKPG..KV.RALYTFEPRTPDEL.FE.GDIIYITDM.D..WWKGTSKGRTGL.PSNYVAEQA
Retrocopy VSKLPPKPVKPG*DKVVRALYTFEPRTPDELCFEAGDIIYITDMNDVSWWKGTSKGRTGLTPSNYVAEQA

Parental  ESIDN-PLHEAAKRGNLSWLR-ECLDNRVGVNGLDKAGSTALYWACHG-GHKDIVEMLFTQPNIELNQQN
          ESIDN....E.AKRGNLSWLR.ECLDNRVGVNGLD.AGSTAL...CHG....DIVEMLFTQP.I...QQN
Retrocopy ESIDN<SMSEGAKRGNLSWLR>ECLDNRVGVNGLDEAGSTALD*VCHG<DFRDIVEMLFTQPRI*PSQQN

Parental  KLGDTALHAAAWKGYADIVQLLLAKGARTDLRNNEKKLAFDMATNAACASLLKKKQGTDAVRTLSNA
          KLGDTALHAAAW.GYADIVQLL.AKG.RT..RNNEKKLA..M..NA...SLL.KKQ.TDAVRTLSNA
Retrocopy KLGDTALHAAAWQGYADIVQLLQAKGVRTG*RNNEKKLALGMVNNAH-GSLL*KKQETDAVRTLSNA

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	19.38 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	16.82 RPM
SRP007412_cerebellum	0.00 RPM	14.21 RPM
SRP007412_heart	0.00 RPM	11.31 RPM
SRP007412_kidney	0.23 RPM	27.70 RPM
SRP007412_liver	0.00 RPM	17.93 RPM
SRP007412_testis	0.04 RPM	9.54 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_836 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_836 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_836 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1058
Pan troglodytes	retro_ptro_720
Gorilla gorilla	retro_ggor_836
Pongo abelii	retro_pabe_883
Callithrix jacchus	retro_cjac_3249

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012808	1 retrocopy	retro_cjac_3249,
Cavia porcellus	ENSCPOG00000007226	1 retrocopy	retro_cpor_1049,
Dipodomys ordii	ENSDORG00000002933	1 retrocopy	retro_dord_698,
Erinaceus europaeus	ENSEEUG00000008320	2 retrocopies	retro_eeur_545, retro_eeur_683,
Felis catus	ENSFCAG00000022374	1 retrocopy	retro_fcat_1869,
Homo sapiens	ENSG00000134996	1 retrocopy	retro_hsap_1058,
Gorilla gorilla	ENSGGOG00000011920	1 retrocopy	retro_ggor_836,
Macaca mulatta	ENSMMUG00000010401	1 retrocopy	retro_mmul_836 ,
Nomascus leucogenys	ENSNLEG00000001854	1 retrocopy	retro_nleu_2502,
Otolemur garnettii	ENSOGAG00000002603	1 retrocopy	retro_ogar_2962,
Pongo abelii	ENSPPYG00000019300	1 retrocopy	retro_pabe_883,
Pan troglodytes	ENSPTRG00000021031	1 retrocopy	retro_ptro_720,
Rattus norvegicus	ENSRNOG00000012156	2 retrocopies	retro_rnor_936, retro_rnor_937,
Sus scrofa	ENSSSCG00000005273	1 retrocopy	retro_sscr_979,
Tursiops truncatus	ENSTTRG00000003081	1 retrocopy	retro_ttru_492,