RetrogeneDB ID: retro_mmul_2346

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 8:65404477..65405484(-)
• Located in intron of: ENSMMUG00000009144

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.4101
• Ensembl ID: ENSMMUG00000001856
• Aliases: None
• Description: None

Sequence

>retro_mmul_2346
TCTCTGGGCATTTATAATCTGGTCCAGAAGGCTCTCAAGCCTTCTCCAATAAAGCTCTATTGGGAAAAAAATGAACCAGT
GAAAATCAAGAAAATCAAAATTTAACACAAATACAGGCAGTTTGCTTCTGCCTAGCGATACCAAGAGATCTCAGATCTAT
GGGAGTCTCAGATTATAATGGAGAAAGAGGAAACAGAAGAGCTAAAACAGTTTGATGATTCAGGTTTGATGCTCATGGGT
TTCAAACCCTTGGTAATGCTGCAGAAGCACAATCACCTGAGGCCATCCCTGTTCATGTGCCCCGAGGAGTTGCTGGTGAT
TGGGAGCTCAACCGTGTTTAGTGCTCTGCACATAAAGTGTCTGGAGAAGGAGGTTGTAGCATTGCGCAGATACGTACCCC
ACAGGAACATGTCTCCTTATTTTGTGGCTTTGGTGCCACAGGAAGAGGATGGAGGACCAGAAAATTCAGGTAACTCCTCC
AGGATTCCAGCTTGTCTTTTTATCCTTTGCTGATGATAAAAGGAAGATGTCCTTTACTGAAAAAGGCATAGCAACTCCAG
AGCAGGTGGACGAGATGAAGGCTATCATTCAGAAGCTCCGCTTCACATACAGAAGTGACAACTTTGAGAACCCCGGGCTG
CAGCAGCACTTCAGGAACCTGGAGGCCTTGGCCTTGGATTTGATGGAGGCTGAATAAGCAGTGGACCTGACATTGCTCTA
AGTTGAAGCAATGATTAAAAGACTGGGCTCCCTGGTGGCTGAGTTTAAGGAGCTTGTTTACCCACCGGATTACAATCCTG
AAGGGAAATTTACCAAGAGAAAACACAATAATGAAGATTTTTGGAAGCAAAAGGCACAAGGCGAAGTATTCAGAAGAGGA
GCTGAAGGCTGATATCTGCAAGGGCACGCTGGGCAAGTTCACTGTGCCCATGCTGAAAGAGGCATACGGGCTGAAGAATG
GGCTGAAGAAGCAGGAGCTGCTGGAAATTCTCACTGAGCACTTCCAG

Alignment

ORF - retro_mmul_2346 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.88 %
• Parental protein coverage: 60.64 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SVGVYNLVQKALKPPPIKLYRETNEPVKTKT-RTFNTSTGGLLLPSDTKRSQIYGS-RQIILEKEETEEL
          S.G.YNLVQKALKP.PIKLY.E.NEPVK.K....FNT.TG.LLLPSDTKRSQIYGS..QII.EKEETEEL
Retrocopy SLGIYNLVQKALKPSPIKLYWEKNEPVKIKK>SKFNTNTGSLLLPSDTKRSQIYGS<SQIIMEKEETEEL

Parental  KRFDDPGLMLMGFKPLVLLKKHHYLRPSLFVYPEESLVIGSSTLFSALLIKCLEKEVAALCRYTPRRNIP
          K.FDD.GLMLMGFKPLV.L.KH..LRPSLF..PEE.LVIGSST.FSAL.IKCLEKEV.AL.RY.P.RN..
Retrocopy KQFDDSGLMLMGFKPLVMLQKHNHLRPSLFMCPEELLVIGSSTVFSALHIKCLEKEVVALRRYVPHRNMS

Parental  PYFVALVPQDEE-LDDQKIQVTPPGFQLVFLPFADDKRKMPFTEKIMATPEQVDKMKAIVEKLRFTYRSD
          PYFVALVPQ.EE...DQKIQVTPPGFQLVFL.FADDKRKM.FTEK..ATPEQVD.MKAI..KLRFTYRSD
Retrocopy PYFVALVPQ-EE>MEDQKIQVTPPGFQLVFLSFADDKRKMSFTEKGIATPEQVDEMKAIIQKLRFTYRSD

Parental  SFENPVLQQHFRNLEALALDLMEPEQAVDLTLPKVEAMNKRLGSLVDEFKELVYPPDYNPEGKVTKRKHD
          .FENP.LQQHFRNLEALALDLME.E.AVDLTL..VEAM.KRLGSLV.EFKELVYPPDYNPEGK.TKRKH.
Retrocopy NFENPGLQQHFRNLEALALDLMEAE*AVDLTLL*VEAMIKRLGSLVAEFKELVYPPDYNPEGKFTKRKHN

Parental  NDG-SGSKRPKVEYSEEELKTHISKGTLGKFTVPMLKEACRAYGLKSGLKKQELLEALTKHFQ
          N....GSKR.K..YSEEELK..I.KGTLGKFTVPMLKEA...YGLK.GLKKQELLE.LT.HFQ
Retrocopy NED>FGSKRHKAKYSEEELKADICKGTLGKFTVPMLKEA---YGLKNGLKKQELLEILTEHFQ

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	179.50 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	156.91 RPM
SRP007412_cerebellum	0.06 RPM	173.32 RPM
SRP007412_heart	0.00 RPM	126.37 RPM
SRP007412_kidney	0.00 RPM	164.55 RPM
SRP007412_liver	0.00 RPM	112.73 RPM
SRP007412_testis	0.08 RPM	388.77 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2346 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2346 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2346 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000196419	4 retrocopies	retro_hsap_4066, retro_hsap_4880, retro_hsap_4913, retro_hsap_511,
Gorilla gorilla	ENSGGOG00000015885	2 retrocopies	retro_ggor_3067, retro_ggor_471,
Macaca mulatta	ENSMMUG00000001856	2 retrocopies	retro_mmul_2346 , retro_mmul_430,
Nomascus leucogenys	ENSNLEG00000015610	3 retrocopies	retro_nleu_1552, retro_nleu_2287, retro_nleu_2676,
Pongo abelii	ENSPPYG00000011876	1 retrocopy	retro_pabe_3821,
Tupaia belangeri	ENSTBEG00000011736	3 retrocopies	retro_tbel_1474, retro_tbel_1523, retro_tbel_3859,
Tursiops truncatus	ENSTTRG00000006749	1 retrocopy	retro_ttru_289,