RetrogeneDB ID: retro_mmul_1010

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 13:112305971..112306769(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDK8
• Ensembl ID: ENSMMUG00000014841
• Aliases: None
• Description: cyclin-dependent kinase 8 [Source:RefSeq peptide;Acc:NP_001248269]

Sequence

>retro_mmul_1010
TTAGCAGATTTGGATCCAGTGATTGTTACATTCTGGTACCGAGCCCCTGAATTACTGCTTTAAGTAAGGCATTATACCAA
AGCTATTGATATTTGGGCTATGGGGTGTATGTTTGAAGAATTACTAATGTCAAAACCAGTATTTCATGGTCGACAAGAGG
ACATCATAACTAGTAATCCTTGTCACCATGACTGGCTGGACAGAATACTCAATGTAATGGGATTTCCTGCAAATAAAGAT
TGGGAAGATGTAAAAAAGATGCCTGAACATTCAACATTAATGAAATATTTCAGAAGAAATAAGTATACTAAACTGCAGCC
TTATCAAGTATATGGAAAAACACAAAGTTAAACCAGATAGTAAAGCATTCCACTTGCTTTAGAAGTTTCTTACCATGGAC
CCAATAAAGTGAATTACCTCAGAACAGATTCCCCATTTCTTAGAAGACCCACTTCCTACATCAGACATTTTTGCCGGTTA
TCAAATCCCTTACCCCAAATCAGAATTTTTAATGGAAGAAGAACCTGATGACAAAGGAGACAAAAGGAACCACCACCAGC
AGCAGGGCAATAACCACATGAATGGAACTGGCCACCCAGGAATCAAGACAACAGTCACACACAGAAGAAAGTGAGGCTTG
TTTCTCCTACCACTACCTCAGGTGGACTTTTCATGGCCTCAGACTATCAGCGTTCCAACACACATACTGCCTATATCCCA
ACCCTGGACCAAGCACATCCCAGCCGAAGAGCAGCATGGGATACTCAGTTACCTCTCAGCAGGCTCCACAGTACTCAC

Alignment

ORF - retro_mmul_1010 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.82 %
• Parental protein coverage: 59.4 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LADLDPVVVTFWYRAPELLLGARHYTKAIDIWAIGCIFAELLTSEPIFHCRQEDIKTSNPYHHDQLDRIF
          LADLDPV.VTFWYRAPELLL..RHYTKAIDIWA.GC.F.ELL.S.P.FH.RQEDI.TSNP.HHD.LDRI.
Retrocopy LADLDPVIVTFWYRAPELLL*VRHYTKAIDIWAMGCMFEELLMSKPVFHGRQEDIITSNPCHHDWLDRIL

Parental  NVMGFPADKDWEDIKKMPEHSTLMKDFRRNTYT-NCSLIKYMEKHKVKPDSKAFHLLQKLLTMDPIKRIT
          NVMGFPA.KDWED.KKMPEHSTLMK.FRRN.YT.NCSLIKYMEKHKVKPDSKAFHLL.K.LTMDPIK.IT
Retrocopy NVMGFPANKDWEDVKKMPEHSTLMKYFRRNKYT>NCSLIKYMEKHKVKPDSKAFHLL*KFLTMDPIK*IT

Parental  SEQAMQDPYFLEDPLPTSDVFAGCQIPYPKREFLTEEEPDDKGDK-NQQQQQGNNHTNGTGHPG-NQDSS
          SEQ....P.FLEDPLPTSD.FAG.QIPYPK.EFL.EEEPDDKGDK.N..QQQGNNH.NGTGHPG.NQD.S
Retrocopy SEQI---PHFLEDPLPTSDIFAGYQIPYPKSEFLMEEEPDDKGDKRNHHQQQGNNHMNGTGHPG<NQDNS

Parental  HTQGPPLKKVRVVPPTTTSGGLIMTSDYQRSNPHAAYPNPGPSTSQPQSSMGYSATSQQPPQYSHQTH
          HTQ....KKVR.V.PTTTSGGL.M.SDYQRSN.H.AY....P...Q...S.......Q.P....H.TH
Retrocopy HTQ----KKVRLVSPTTTSGGLFMASDYQRSNTHTAYI---PTLDQAHPSRRAAWDTQLPLSRLHSTH

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	16.47 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	10.07 RPM
SRP007412_cerebellum	0.00 RPM	40.23 RPM
SRP007412_heart	0.00 RPM	11.72 RPM
SRP007412_kidney	0.12 RPM	13.15 RPM
SRP007412_liver	0.00 RPM	8.27 RPM
SRP007412_testis	0.00 RPM	36.98 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1010 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1010 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1010 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2147

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001443	1 retrocopy	retro_chof_1102,
Homo sapiens	ENSG00000132964	1 retrocopy	retro_hsap_2147,
Myotis lucifugus	ENSMLUG00000009176	1 retrocopy	retro_mluc_112,
Macaca mulatta	ENSMMUG00000014841	1 retrocopy	retro_mmul_1010 ,
Mus musculus	ENSMUSG00000029635	1 retrocopy	retro_mmus_1200,
Nomascus leucogenys	ENSNLEG00000014010	1 retrocopy	retro_nleu_2746,