RetrogeneDB ID: retro_mmul_1651

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:181408721..181409698(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.10117
• Ensembl ID: ENSMMUG00000006171
• Aliases: None
• Description: monocarboxylate transporter 1 [Source:RefSeq peptide;Acc:NP_001244633]

Sequence

>retro_mmul_1651
ATGCCACCAGCAGTTGGAAGTTAAGTTGGATACACCCCTTCAGACGGAGGTTGGGGTGGGCAGTTTAGTGGAAGCTTTCA
TTTCCATCAACTTCTCTCAGCATTTCTCAAATATATTACTGTTTTCTTCAAAGAGATGGAAGGTCTATTCCATGCCACCA
CCAGCGAAGTGTTACAGATGTGCTCCGTCATGCTGGCTGTTACGTAAGGTGGAGGTCTCATCAGCAGTATCTTGGTGAAT
AATGCGACAGTCGTTCAGTCATGACTGTTGGTGTTGCTTGTCAGGCTGTGGTTGATTGTGGCTTCTTTCTGTAACATTAT
GCAGGAACTTTACTTGTGTATTGGAATCATTGGAGGTCTTGGGCTTTCCTTTAACTTGAACCTAGCTTTGACCATGATTG
GCAAGCATTTCTATATGAAGTGACCACTGGCCATCAGACTGGCCATGGCGGGCAGCCTCTCTATGCTGGCCCCCTCAATC
AGGCTTTCTTTGGTATCTGTGGATGGAGAGGAAGCTTCCTAACTCTTGGGGGCTTCCTACTAAACTGCTGTGTAGCTAGA
GACCTGATGTGACCAATAACGTCCAAGCCAACGAAGGCAGGGAAAGAGGTCTAAAGAATTCCTTCAGGAAGCCGAAAAAT
CAGATGCAAAGAAAGGTACAGGTGATACAAATACAGATATTATTGGAGGACACCCCAAAGAAGGGAAATGATTAATCTTC
CAAACAATTAATACATTCCTGTACTTATCCCTGTTTACTCAGAGAGATTTTTTGCTGTATCTCTCTGGAAATGTGCTCAC
ATTTTTCTGGACTCTTTACACCTTTGGCGTTTCTTAATAATTATGACAAGAGTCGGTATCATTCCAGGAGCACTCTGCCT
TCCTTCTTTCCCTTCTGGCTTTTGTTGATACACAGCAAGGACTTCTATGGGACTTGCAGCCAACAGAAAGCGGATAAGGT
CTCAGGTTCTCAAGTTC

Alignment

ORF - retro_mmul_1651 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.89 %
• Parental protein coverage: 66.4 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 11

Retrocopy - Parental Gene Alignment:

Parental  MPPAVGGPVGYTPPDGGWG-WAV-VIGAFISIGFSY-AFPKSITVFFKEIESIFHATTSEVSWISSIMLA
          MPPAVG..VGYTP.DGGWG.WAV....AFISI.FS..AF.K.ITVFFKE.E..FHATTSEV....S.MLA
Retrocopy MPPAVGS*VGYTPSDGGWG<WAV<LVEAFISINFSQ<AFLKYITVFFKEMEGLFHATTSEVLQMCSVMLA

Parental  VMYGGGPISSILVNKY-GSRIVMIIGG-CLSGCG-LIAASFCNTVQELYFCIGFVGGLGLAFNLNPALTM
          V..GGG.ISSILVN....SR.VM..G..CLSGCG.LI.ASFCN..QELY.CIG..GGLGL.FNLN.ALTM
Retrocopy VT*GGGLISSILVNNA<DSRSVMTVGV<CLSGCG<LIVASFCNIMQELYLCIGIIGGLGLSFNLNLALTM

Parental  IGKYFYKRRPLANGLAMA-GSPVFLCTLAPLNQVFFGIFGWRGSFLILGGLLLNCCVAGALMRPIGPKPT
          IGK.FY...PLA..LAMA.G.P.......PLNQ.FFGI.GWRGSFL.LGG.LLNCCVA..LM.PI..KPT
Retrocopy IGKHFYMK*PLAIRLAMA<GQPLYA---GPLNQAFFGICGWRGSFLTLGGFLLNCCVARDLM*PITSKPT

Parental  KA-GKDKSKASLQKAGKSGVKKGRHDANTDLIGRHPKREKRSVFQTINQFLDLTLFTHRGFLLYLSGNVI
          KA.GK..SK..LQ.A.KS..KKG..D.NTD.IG.HPK..K...FQTIN.FL.L.LFT.R.FLLYLSGNV.
Retrocopy KA>GK-RSKEFLQEAEKSDAKKGTGDTNTDIIGGHPKEGK*LIFQTINTFLYLSLFTQRDFLLYLSGNVL

Parental  MFF-GLFAPLVFLSSYGKSQHYS-SEKSAFLLSILAFVD-MVARPSMGLVANTKPIRPRIQYF
          .FF.GLF.PL.FL..Y.KS...S..E.SAFLLS.LAFVD...AR.SMGL.AN.K.IR.....F
Retrocopy TFF>GLFTPLAFLNNYDKSRYHS<QEHSAFLLSLLAFVD<YTARTSMGLAANRKRIRSQVLKF

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	10.08 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	8.65 RPM
SRP007412_cerebellum	0.06 RPM	21.31 RPM
SRP007412_heart	0.00 RPM	100.75 RPM
SRP007412_kidney	0.12 RPM	10.92 RPM
SRP007412_liver	0.00 RPM	11.16 RPM
SRP007412_testis	0.00 RPM	58.61 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1651 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1651 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1651 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000006171	1 retrocopy	retro_mmul_1651 ,