RetrogeneDB ID: retro_mmul_87

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:134149622..134150492(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000007924
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: E2F6
• Ensembl ID: ENSMMUG00000023225
• Aliases: None
• Description: transcription factor E2F6 [Source:RefSeq peptide;Acc:NP_001253584]

Sequence

>retro_mmul_87
ATGAGTCAACAGCAGCCTGCAGGAAAGTTGACCAACCTGCCCATTAACCCGGCAGAGGAGACGGTTCGCCGCCGAGACGC
CACCAATGCAGAGTACCCATCGCCATCAACAATAAGCATTAATTCCAAAGATGATGTACAACCTGAGTCTGAAAGAGAAA
CTGTAAATATGAAACCTCATAATAAGGCATCACTGGCTTGTACAACACGAAAATTTATAGATATTCTCAAATCAGCTCCT
GGAGGTGTTCTTAACTTAAGCCAGGTTGCAGCAAAACTGGCAGTGCACAGACGAAGAATATATGACATCGTCAGTGTCTT
AGAAGGAGTCAAACTAATTAAAAAAATGCCTAAGAACCATATTCAGTGGATTGGACCTGATTTTAATTCTGGAGCAACAC
CCGAAGAAAAAAAGTTAGAGGAGGAACTTTCCAAATTATCAGCAACAGAAGATGCCTTGGATAAGCTAATTGGAGATTGT
TCTCAGCAACTGTGTGAGTTAACAAATGACAAAGAATTGGGAAAACTAGCATATGTTACGCATGAAGACATTCACCACTT
GGAACCTTTCCAGGAACAGACCATTTTTGTAGTTAGCGCGCCGGTAGAAATCACACTGGAAATTCCAGTTTCTGAAGACT
CTTTCTTATTACATGTAAATAACACCAATGGACCTGGTAACGCCTGTTTGTGTCTATTGAAGAAAGATTACGAAGATAAC
TGCACGTCTGAGGGTGCCGGGACTTCATCTGAGGGTGCCGGGACTTCATCTGAGAGCACTGGGACTTCATCTGAGATCGG
ATGTACAGAACGCCCTGAAGAAGAAGAAAGTCCTCAGCAAAGTGAAAAATTGCTTGACATGAGCAACTGA

Alignment

ORF - retro_mmul_87 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.53 %
• Parental protein coverage: 90.81 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSQQRPARKLPSLLLDPAEETVRRRCRDPINVEGLLPSKIRINLEDNVQYVSMRKALKVKRPRFDVSLVY
          MSQQ.PA.KL..L...PAEETVRRR..D..N.E...PS.I.IN..D.VQ..S.R.....K.P....SL..
Retrocopy MSQQQPAGKLTNLPINPAEETVRRR--DATNAEYPSPSTISINSKDDVQPESERETVNMK-PHNKASLAC

Parental  LTRKFMDLVRSAPGGILDLNKVATKLGVRKRRVYDITNVLDGIDLVEKKSKNHIRWIGSDLSNFGAVPQQ
          .TRKF.D...SAPGG.L.L..VA.KL.V..RR.YDI..VL.G..L..K..KNHI.WIG.D..N.GA.P..
Retrocopy TTRKFIDILKSAPGGVLNLSQVAAKLAVHRRRIYDIVSVLEGVKLIKKMPKNHIQWIGPDF-NSGATPEE

Parental  KKLQEELSDLSAMEDALDELIKDCAQQLFELTDDKENERYPLTYVTYQDIHSIQAFHEQIVIAVKAPAET
          KKL.EELS.LSA.EDALD.LI.DC.QQL.ELT.DKE.....L.YVT..DIH....F.EQ....V.AP.E.
Retrocopy KKLEEELSKLSATEDALDKLIGDCSQQLCELTNDKELGK--LAYVTHEDIHHLEPFQEQTIFVVSAPVEI

Parental  RLDVPAPREDSITVHIRSTNGPIDVYLCEVEQGQTGSKRSEGVGTSS
          .L..P...EDS...H...TNGP....LC...........SEG.GTSS
Retrocopy TLEIPV-SEDSFLLHVNNTNGPGNACLCLLKKDYEDNCTSEGAGTSS

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	13.67 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	8.88 RPM
SRP007412_cerebellum	0.00 RPM	12.98 RPM
SRP007412_heart	0.06 RPM	8.66 RPM
SRP007412_kidney	0.00 RPM	9.98 RPM
SRP007412_liver	0.00 RPM	3.80 RPM
SRP007412_testis	0.15 RPM	5.50 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_87 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_87 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_87 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4906

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000048286	1 retrocopy	retro_btau_1820,
Callithrix jacchus	ENSCJAG00000006910	1 retrocopy	retro_cjac_178,
Dasypus novemcinctus	ENSDNOG00000000258	1 retrocopy	retro_dnov_187,
Homo sapiens	ENSG00000169016	4 retrocopies	retro_hsap_2542, retro_hsap_2547, retro_hsap_2572, retro_hsap_4906,
Macropus eugenii	ENSMEUG00000007957	4 retrocopies	retro_meug_1169, retro_meug_860, retro_meug_882, retro_meug_893,
Myotis lucifugus	ENSMLUG00000003384	1 retrocopy	retro_mluc_864,
Macaca mulatta	ENSMMUG00000017649	1 retrocopy	retro_mmul_955,
Macaca mulatta	ENSMMUG00000023225	1 retrocopy	retro_mmul_87 ,
Nomascus leucogenys	ENSNLEG00000014134	1 retrocopy	retro_nleu_2351,
Pongo abelii	ENSPPYG00000012646	1 retrocopy	retro_pabe_1,
Pan troglodytes	ENSPTRG00000011661	2 retrocopies	retro_ptro_1484, retro_ptro_3272,
Ictidomys tridecemlineatus	ENSSTOG00000003316	1 retrocopy	retro_itri_135,