RetrogeneDB ID: retro_mmul_216

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 9:46158421..46159306(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000030594
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: MMU.14275
• Ensembl ID: ENSMMUG00000020214
• Aliases: None
• Description: survival of motor neuron 1, telomeric [Source:RefSeq peptide;Acc:NP_001247593]

Sequence

>retro_mmul_216
ATGGCCATGAGCAGCGGCGGCAGTGGTGGCGGGGTCCGGGAGCAGGAGGATTCCCTGCTGTTTGGGCGGGGCACAGGCCA
GAGCGATGATTCTGACATTTGGGATGATACGGCACTGATAAAAGCATATGATAAAGCTGTGGCTTCATTTAAGCATGCTC
TAAAGAATGGTGACATTTGTGAAACTCCAGGTAAACCAAAAACCACACCTAAAAGAAAACCTGCTAAGAAGAATAAACGC
CAAAAGAAGAATACTGCAGCTCCCTTAAAACAGTGGAAAGTTGGGGACAAATATTCTGTCATTTGGTCAGAAGACGGTTG
CATTTACCCAGCTACCATTGCTTCAGTTGATTTTAAGAGAGAAACCTGTGTTGTGGTTTACTCTCGATATGGCAATAGAG
AGGAGCAAAATCTGTTGGATCTACTTTCCCCAATCTCTGAAGTAGCTAACAATATAGAACAGAATGCTCAAGAGAATGAA
AATGAAAGCCGAGTTTCAACAGATGAAAGTGAGAATTCCAGGTCTCCTGGAAATAAATCAGATAACATCAAGTCCAAATC
TGCTCCGTGGAACTCTTTTCTCCCTCCACCACCCCCCATGCCAGGGCCAAGACTTGGACCAGGAAAGCCAGGTCTAAAAT
TCAATGGCCCACCACCACCCCCGCCAGCACCACCACCTCACTTACTATCATGCTGGCTGCCTCCATTTCCTTCTAGACCA
CCAAAAATTCCCCCACCACCTCCCATATGTCCAGATTCTCTTGATGAGGCTGATGCTTTGGGAAGTATGTTAATTTTGTG
GTACATGAGAGGCTATCATACTGGCTATTACATGGGTTTCAGACAAAATCAAAAAGAAGGAAGATGCTCACATTCCTTAA
ATTAA

Alignment

ORF - retro_mmul_216 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.54 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAMSSGGSGGGVPEQEDSVLFRRGTGQSDDSDIWDDTALIKAYDKAVASFKHALKNGDICETSGKPKTTP
          MAMSSGGSGGGV.EQEDS.LF.RGTGQSDDSDIWDDTALIKAYDKAVASFKHALKNGDICET.GKPKTTP
Retrocopy MAMSSGGSGGGVREQEDSLLFGRGTGQSDDSDIWDDTALIKAYDKAVASFKHALKNGDICETPGKPKTTP

Parental  KRKPAKKNKSQKKNTAAPLKQWKVGDKCSAIWSEDGCIYPATIASVDFKRETCVVVYTGYGNREEQNLSD
          KRKPAKKNK.QKKNTAAPLKQWKVGDK.S.IWSEDGCIYPATIASVDFKRETCVVVY..YGNREEQNL.D
Retrocopy KRKPAKKNKRQKKNTAAPLKQWKVGDKYSVIWSEDGCIYPATIASVDFKRETCVVVYSRYGNREEQNLLD

Parental  LLSPISEVANNIEQNAQENENESQVSTDESENSRSPGSKSDNIKSKSAPWNSFLPPPPPMPGPRLGPGKP
          LLSPISEVANNIEQNAQENENES.VSTDESENSRSPG.KSDNIKSKSAPWNSFLPPPPPMPGPRLGPGKP
Retrocopy LLSPISEVANNIEQNAQENENESRVSTDESENSRSPGNKSDNIKSKSAPWNSFLPPPPPMPGPRLGPGKP

Parental  GLKFNGPPPPPPPPPPHLLSCWMPPFPSGPPIIPPPPPICPDSLDDADALGSMLISWYMSGYHTGYYMGF
          GLKFNGPPPPPP.PPPHLLSCW.PPFPS.PP.IPPPPPICPDSLD.ADALGSMLI.WYM.GYHTGYYMGF
Retrocopy GLKFNGPPPPPPAPPPHLLSCWLPPFPSRPPKIPPPPPICPDSLDEADALGSMLILWYMRGYHTGYYMGF

Parental  RQNQKEGRCSHSLN
          RQNQKEGRCSHSLN
Retrocopy RQNQKEGRCSHSLN

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	0.11 RPM	5.94 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	4.60 RPM
SRP007412_cerebellum	0.06 RPM	5.94 RPM
SRP007412_heart	0.00 RPM	3.24 RPM
SRP007412_kidney	0.00 RPM	4.46 RPM
SRP007412_liver	0.00 RPM	1.46 RPM
SRP007412_testis	0.00 RPM	11.61 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_216 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_216 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_216 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000012328	1 retrocopy	retro_cpor_988,
Dasypus novemcinctus	ENSDNOG00000007283	4 retrocopies	retro_dnov_1239, retro_dnov_1613, retro_dnov_1637, retro_dnov_2175,
Echinops telfairi	ENSETEG00000001406	2 retrocopies	retro_etel_1549, retro_etel_2012,
Homo sapiens	ENSG00000205571	1 retrocopy	retro_hsap_4140,
Gorilla gorilla	ENSGGOG00000026704	1 retrocopy	retro_ggor_2780,
Myotis lucifugus	ENSMLUG00000010603	1 retrocopy	retro_mluc_1623,
Macaca mulatta	ENSMMUG00000020214	1 retrocopy	retro_mmul_216 ,
Nomascus leucogenys	ENSNLEG00000004454	1 retrocopy	retro_nleu_1054,
Oryctolagus cuniculus	ENSOCUG00000017097	1 retrocopy	retro_ocun_617,
Pan troglodytes	ENSPTRG00000016955	1 retrocopy	retro_ptro_2813,
Sus scrofa	ENSSSCG00000016970	1 retrocopy	retro_sscr_654,
Ictidomys tridecemlineatus	ENSSTOG00000012288	1 retrocopy	retro_itri_968,
Tupaia belangeri	ENSTBEG00000002399	1 retrocopy	retro_tbel_1033,