RetrogeneDB ID: retro_mmul_1869

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 5:8149282..8150839(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.142
• Ensembl ID: ENSMMUG00000022686
• Aliases: None
• Description: None

Sequence

>retro_mmul_1869
CTGGGATACATCACCCTTTATCTGGAGAAGGAACGAGAGAAAGAAATTAGTGATTATAAGGCAGAGGAAGAGAAAGGTGA
GAAAGAAGAGGAAAATAAAGATGATGAAGAAAAGCCCAAGATCAAAGATGTGGGTTCAGATGAGGAGGATGACAGTGGTA
AGGGTAAGAAGAAGAAAACTAAGATCAAAGAGAAATACATTGATCAAGAAGAACTAAACAAGACCAAGCCTGTTTAGACC
AGAAACCCTGAAGACATCACCCAAGAGGAGTATGGAGAATTCTACAAGAGCCTCACCAATGACTGAGAATACCACTTGGC
AGTCAGGCACTTTTCTGTAGAAGGTCAGTTGGAATTCAGGGCATTGTTATTCATTCCTCACGGGGCTCCCTTTGATCTTT
TTGAGAACAAGAAGAAAAAGAACAACATCAAACTCTATGTCCATCGTGTGTTCATCAGGGACAGCTGTGATGAGTTGATA
CCAGAGTGTCTCAACTTTACCCGTGGTGTGGTTGACTCTGAGAATTTGCCCCTGAACATCTCCCAAGAAATGCTCCAGCA
GAACAAAATCTTGAAAGTCATTCACAGAAACATTGTTAAGAAGTGCCTTGAGCTCTTTGCTGAGCTGGTGGAAGGCAAGG
ACAATTACAAGAAATTCTATGAGAAATTCTCTAAAAATCTCAAGCTTAGGATCCACAAGGATTCCACTAACCTATGCCGC
CTGTCTGAGCTGCTGTGCTATCACAGCTCCTGGTCTGGAGATGAGATGACTTCTTTGTCAAGTATGTTTCTCGCATGAAG
AAGATACAGAAGTCCATCTATTACATCACTGGTGAGAGCAAAGAGCAGGTTGCCAACTCAGCTTTTGTGGAGGGAGTGTG
GAAGCAGGGCTTCGAGGTGGTATATATGACTGAGCCCATTGATGGCTATGTGTGCAGCAACTCAAGGAGTTTGATGGGAA
GAGCCTGGACTTAGTTACCAAGGAGGGTCTGGAACTACCTGAGGATGAAGAGAAGAAGAGAATGGAAGAGAGGAAGGCAA
AGTTTGAGAACCTCTGCAAGCTCATGAAAGAAATCTTAGATAAGAAGATTGAGAAGGTGACAATCTCCAGTAGGCTTGTG
TCTTCACCCTGCTGCATTGTGACCAGCACCTACAGCTGGACAGCCAATATGGAGCAGATCATGAAAGCCCAGGCACTTCG
GGTCAACTCCACCATGAGCTATATGATGGCCAAAAAGCACCTGGAGATCAACCCTGACCACCCCATTGTGGAGACGCTGC
AGCAAAAGGCTGAGGCAGACAAGAATGACAAGGCAGTCAAGGACCTGGTGGTGCTGCTGTTAGAAACTGCCTTGCTCTCT
TCTGGCTTTTCCCTTGAGGATCCCCAGACCCACTCCAACCGCATCTACTGCATGATCAAGCTAGGTCTAGGTATCAATGA
AGATTAAGTGGCAGCAGAGGAACACAGTGCTGTGGTTCCTGATGAGATCGCCCCTCTTGAGGGTGACAAGGATGTGTCTC
GCATGGAAGAAGTAGATTAGGAATTCATAGTTGGAAA

Alignment

ORF - retro_mmul_1869 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.08 %
• Parental protein coverage: 70.98 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  IGYPITLYLEKEREKEISDDEAEEEKGEKEEEDKDDEEKPKIEDVGSDEEDDSGKDKKKKTKKIKEKYID
          .GY.ITLYLEKEREKEISD....................PKI.DVGSDEEDDSGK.KKKKTK.IKEKYID
Retrocopy LGY-ITLYLEKEREKEISDYKXXXXXXXXXXXXXXXXXXPKIKDVGSDEEDDSGKGKKKKTK-IKEKYID

Parental  QEELNKTKPIWTRNPDDITQEEYGEFYKSLTNDWEDHLAVKHFSVEGQLEFRALLFIPRRAPFDLFENKK
          QEELNKTKP..TRNP.DITQEEYGEFYKSLTND.E.HLAV.HFSVEGQLEFRALLFIP..APFDLFENKK
Retrocopy QEELNKTKPV*TRNPEDITQEEYGEFYKSLTND*EYHLAVRHFSVEGQLEFRALLFIPHGAPFDLFENKK

Parental  KKNNIKLYVRRVFIMDSCDELIPEYLNFIRGVVDSEDLPLNISREMLQQSKILKVIRKNIVKKCLELFSE
          KKNNIKLYV.RVFI.DSCDELIPE.LNF.RGVVDSE.LPLNIS.EMLQQ.KILKVI..NIVKKCLELF.E
Retrocopy KKNNIKLYVHRVFIRDSCDELIPECLNFTRGVVDSENLPLNISQEMLQQNKILKVIHRNIVKKCLELFAE

Parental  LAEDKENYKKFYEAFSKNLKLGIHEDSTNRRRLSELLRYHTSQSGDEMTSLS-EYVSRMKETQKSIYYIT
          L.E.K.NYKKFYE.FSKNLKL.IH.DSTN..RLSELL.YH.S.SGDEMTSLS..YVSRMK..QKSIYYIT
Retrocopy LVEGKDNYKKFYEKFSKNLKLRIHKDSTNLCRLSELLCYHSSWSGDEMTSLS<KYVSRMKKIQKSIYYIT

Parental  GESKEQVANSAFVERVRKRGFEVVYMTEPIDEY-CVQQLKEFDGKSLVSVTKEGLELPEDEEEKKKMEES
          GESKEQVANSAFVE.V.K.GFEVVYMTEPID.Y.CVQQLKEFDGKSL..VTKEGLELPED.EEKK.MEE.
Retrocopy GESKEQVANSAFVEGVWKQGFEVVYMTEPIDGY<CVQQLKEFDGKSLDLVTKEGLELPED-EEKKRMEER

Parental  KAKFENLCKLMKEILDKKVEKVTISNRLVSSPCCIVTSTYGWTANMERIMKAQALRDNSTMGYMMAKKHL
          KAKFENLCKLMKEILDKK.EKVTIS.RLVSSPCCIVTSTY.WTANME.IMKAQALR.NSTM.YMMAKKHL
Retrocopy KAKFENLCKLMKEILDKKIEKVTISSRLVSSPCCIVTSTYSWTANMEQIMKAQALRVNSTMSYMMAKKHL

Parental  EINPDHPIVETLRQKAEADKNDKAVKDLVVLLFETALLSSGFSLEDPQTHSNRIYRMIKLGLGIDEDEVA
          EINPDHPIVETL.QKAEADKNDKAVKDLVVLL.ETALLSSGFSLEDPQTHSNRIY.MIKLGLGI.ED.VA
Retrocopy EINPDHPIVETLQQKAEADKNDKAVKDLVVLLLETALLSSGFSLEDPQTHSNRIYCMIKLGLGINED*VA

Parental  AEEPSAAVPDEI-PL-RAMRMRLAWKKSIR-VHSWK
          AEE.SA.VPDEI.PL.R..RM.LAWKK.IR..HSWK
Retrocopy AEEHSAVVPDEI>PLLRVTRMCLAWKK*IR>IHSWK

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	1230.31 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	1089.76 RPM
SRP007412_cerebellum	0.13 RPM	787.49 RPM
SRP007412_heart	0.06 RPM	930.98 RPM
SRP007412_kidney	0.00 RPM	474.76 RPM
SRP007412_liver	0.00 RPM	314.65 RPM
SRP007412_testis	0.19 RPM	376.63 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1869 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1869 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1869 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2912
Pan troglodytes	retro_ptro_1968
Pongo abelii	retro_pabe_2425

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001981	4 retrocopies	retro_cfam_1108, retro_cfam_411, retro_cfam_562, retro_cfam_881,
Felis catus	ENSFCAG00000009764	1 retrocopy	retro_fcat_1177,
Homo sapiens	ENSG00000096384	2 retrocopies	retro_hsap_2912, retro_hsap_2958,
Macropus eugenii	ENSMEUG00000013735	1 retrocopy	retro_meug_1896,
Myotis lucifugus	ENSMLUG00000005239	2 retrocopies	retro_mluc_1604, retro_mluc_865,
Macaca mulatta	ENSMMUG00000011073	2 retrocopies	retro_mmul_1526, retro_mmul_2313,
Macaca mulatta	ENSMMUG00000022686	2 retrocopies	retro_mmul_1319, retro_mmul_1869 ,
Macaca mulatta	ENSMMUG00000023469	1 retrocopy	retro_mmul_391,
Mus musculus	ENSMUSG00000023944	3 retrocopies	retro_mmus_1916, retro_mmus_3528, retro_mmus_856,
Rattus norvegicus	ENSRNOG00000019834	6 retrocopies	retro_rnor_1561, retro_rnor_1562, retro_rnor_1787, retro_rnor_597, retro_rnor_598, retro_rnor_87,
Tursiops truncatus	ENSTTRG00000006924	1 retrocopy	retro_ttru_292,