RetrogeneDB ID: retro_mmul_1357

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 18:61917665..61918145(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.3225
• Ensembl ID: ENSMMUG00000013098
• Aliases: None
• Description: None

Sequence

>retro_mmul_1357
ATGGCCACCTTCGTAGAGCTCAGTATCAAAGACAAGATGGCCATCATAGGCCTGGACACCTGGCAGTCTCCTCCAGGCAA
AGTTGAATAAACTGTGAAGGTGGCCCTTGATGTGAGATATTGCCACATTGACTGTGCCTGTCTATAAGAATGAAGATGAG
GTGAGGAAGCCATCTAGGAGAATATCCAAGAGAATGCTGTCGAACAGGAGTACCGCTTTATCATTGGCAAGTTGAGGCCC
ACCTTCTTTGAGAGACCCCTTGTGAAGGAGGCCTGTCAGAAGACCCTCAAGTACCTGAAACTGAACTACCTGGACATCTA
TTTTATTCACCGGACACAGGGATTCCAGCCCTGGCAGTAGGTTCTCCCCAAAGATGATAAAGGTAATGTCATCAGCAGTA
AAGCATTCTTTGTTGCTTGGGAGGCCATGCATGAGGTGGTGGACAAAGGGCTGGTGAATATTCTCTAACTTCAATTATTT

Alignment

ORF - retro_mmul_1357 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.58 %
• Parental protein coverage: 51.27 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MATFVELSTKAKMPIVGLGTWKSPLGKVKEAVKVAIDAGYRHIDCAYVYQ---NEHEVGEAIQEKIQEQA
          MATFVELS.K.KM.I.GL.TW.SP.GKV...VKVA.D..Y.HIDCA........E....E.IQE.....A
Retrocopy MATFVELSIKDKMAIIGLDTWQSPPGKVE*TVKVALDVRYCHIDCACL*E*R*GEEAI*ENIQE----NA

Parental  VKREDLFIVSKLWPTFFERPLVRKAFEKTLKDLKLSYLDVYLIHWPQGFKSGDDILPKDDKDNVIGGKAT
          V..E..FI..KL.PTFFERPLV..A..KTLK.LKL.YLD.Y.IH..QGF......LPKDDK.NVI..KA.
Retrocopy VEQEYRFIIGKLRPTFFERPLVKEACQKTLKYLKLNYLDIYFIHRTQGFQPWQ*VLPKDDKGNVISSKAF

Parental  FLDAWEAMEELVDEGLVKALGISNF
          F..AWEAM.E.VD.GLV..L....F
Retrocopy FV-AWEAMHEVVDKGLVNIL*LQLF

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	4.37 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	4.13 RPM
SRP007412_cerebellum	0.00 RPM	2.71 RPM
SRP007412_heart	0.00 RPM	29.62 RPM
SRP007412_kidney	0.00 RPM	8.57 RPM
SRP007412_liver	0.00 RPM	48.77 RPM
SRP007412_testis	0.00 RPM	6.56 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1357 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1357 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1357 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000166	1 retrocopy	retro_chof_400,
Callithrix jacchus	ENSCJAG00000012250	1 retrocopy	retro_cjac_3038,
Erinaceus europaeus	ENSEEUG00000004422	1 retrocopy	retro_eeur_681,
Echinops telfairi	ENSETEG00000006005	3 retrocopies	retro_etel_1055, retro_etel_1643, retro_etel_748,
Homo sapiens	ENSG00000198074	1 retrocopy	retro_hsap_581,
Macaca mulatta	ENSMMUG00000013098	2 retrocopies	retro_mmul_1357 , retro_mmul_2455,
Mus musculus	ENSMUSG00000029762	1 retrocopy	retro_mmus_627,
Mus musculus	ENSMUSG00000052131	1 retrocopy	retro_mmus_2860,
Mus musculus	ENSMUSG00000061758	1 retrocopy	retro_mmus_1490,
Nomascus leucogenys	ENSNLEG00000013088	1 retrocopy	retro_nleu_801,
Pongo abelii	ENSPPYG00000018018	1 retrocopy	retro_pabe_606,
Pan troglodytes	ENSPTRG00000019718	1 retrocopy	retro_ptro_428,
Rattus norvegicus	ENSRNOG00000009734	3 retrocopies	retro_rnor_2380, retro_rnor_2588, retro_rnor_657,
Sorex araneus	ENSSARG00000001396	1 retrocopy	retro_sara_608,