RetrogeneDB ID: retro_mmul_728

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1099214756228:614..937(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.3227
• Ensembl ID: ENSMMUG00000011827
• Aliases: None
• Description: cyclin-dependent kinase 2-associated protein 2 [Source:RefSeq peptide;Acc:NP_001253515]

Sequence

>retro_mmul_728
ATGTCCTACAAACCCATCACACCTGCCCCCAGCAGCACCCCCGGCTCCAGCACCCCTGGGCTGGGCACCCCGGTCCCTAC
AGGAAGCGTCCCTTCACCGTCGGGCTCGGTGCCAGAAGCTGCTGTCCCTTTCAAACCGCTATTTAACGACTTTGGACCGC
CTCCATCGGCTGCATGCAGGCCATGAAACCACCTGGCGCCCAGGGTTCCCAGAGCACCCACAGGGAACTGCTGTCGGTCA
GAGGGGAGATGGGCAAAGGGATCCGGACCACCTTTGCTGGCAGCAAGAGCACCACGGAGCACCTGAAGAGAGAGATCATC
CAT

Alignment

ORF - retro_mmul_728 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.73 %
• Parental protein coverage: 85.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSYKPIAPAPSSTPGSSTPGPGTPVPTGSVPSPSGSVPGAAAPFRPLFNDFGPP-SMGYVQAMKPPGAQG
          MSYKPI.PAPSSTPGSSTPG.GTPVPTGSVPSPSGSVP.AA.PF.PLFNDFGPP.S.G..QAMKPPGAQG
Retrocopy MSYKPITPAPSSTPGSSTPGLGTPVPTGSVPSPSGSVPEAAVPFKPLFNDFGPP<SIGCMQAMKPPGAQG

Parental  SQSTYTDLLSVIEEMGKEIRPTYAGSKSAMERLKRGIIH
          SQST...LLSV..EMGK.IR.T.AGSKS..E.LKR.IIH
Retrocopy SQSTHRELLSVRGEMGKGIRTTFAGSKSTTEHLKREIIH

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	5.15 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	22.69 RPM
SRP007412_cerebellum	0.00 RPM	5.17 RPM
SRP007412_heart	0.00 RPM	10.42 RPM
SRP007412_kidney	0.00 RPM	13.97 RPM
SRP007412_liver	0.00 RPM	38.40 RPM
SRP007412_testis	0.00 RPM	1.66 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_728 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_728 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_728 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000011370	1 retrocopy	retro_cfam_55,
Equus caballus	ENSECAG00000020079	2 retrocopies	retro_ecab_180, retro_ecab_579,
Echinops telfairi	ENSETEG00000006428	3 retrocopies	retro_etel_257, retro_etel_334, retro_etel_437,
Homo sapiens	ENSG00000167797	4 retrocopies	retro_hsap_3699, retro_hsap_4172, retro_hsap_4176, retro_hsap_4268,
Gorilla gorilla	ENSGGOG00000010159	3 retrocopies	retro_ggor_2502, retro_ggor_2799, retro_ggor_2800,
Macaca mulatta	ENSMMUG00000000434	1 retrocopy	retro_mmul_1507,
Macaca mulatta	ENSMMUG00000011827	5 retrocopies	retro_mmul_1712, retro_mmul_640, retro_mmul_728 , retro_mmul_730, retro_mmul_763,
Nomascus leucogenys	ENSNLEG00000006438	1 retrocopy	retro_nleu_176,
Otolemur garnettii	ENSOGAG00000008275	1 retrocopy	retro_ogar_1584,
Pan troglodytes	ENSPTRG00000003966	9 retrocopies	retro_ptro_2508, retro_ptro_2973, retro_ptro_2976, retro_ptro_3002, retro_ptro_3003, retro_ptro_3004, retro_ptro_3005, retro_ptro_3008, retro_ptro_3009,
Tupaia belangeri	ENSTBEG00000005476	2 retrocopies	retro_tbel_439, retro_tbel_612,