RetrogeneDB ID: retro_mmul_501

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:66153994..66155360(-)
• Located in intron of: ENSMMUG00000032060

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.10030
• Ensembl ID: ENSMMUG00000016118
• Aliases: None
• Description: dnaJ homolog subfamily C member 7 [Source:RefSeq peptide;Acc:NP_001248180]

Sequence

>retro_mmul_501
TTCAAGGAACAAGGAAATGCATATTATGTGAAGAAAGATTACAACGAAGCTTACAATTATACAAAAGCCTTAGGCATATG
TCCTAAAAATACTAGCTATTACAGTAATCAAGCAGCCACATTGATTATGCTTGGAAGGTTCCAGGAAGCTCTTGGAGATG
CACACCAGTCATTGAGATTGGATGACAGTTTTGTTCAGGGACATCTAGGAGAGGGCAAGTGCCCCCTCTCTCCCTAGAGA
ATGCCATGGCCATATGTCAGTTTCCAGAGAGCCCTAGAACTGGATCATAAAAATGCTCAGGAATAACAGGAGTTCAAGAA
TGCTAATTCAATCATGGAATATGAGAAGTTAGCAAAAACAGATTTTGAGAAGCATGATATTAGAAAGGTTGTTCTCTGCA
TGGACTGTGCCCTCCTACTTGCCCCTGCCTGCCATTGCTTCAAAATCCTCAAAGCAGAATATTTAGTAATGCTGGGTCAT
ATCCAGAAGCACAATCTGTAGCCAGTGACATTTTACAAATGGAGTCCACCAATGCAGATCCTCTGTATGTGTAAGGTCTT
TGCCTTTATTATGAAGATTGTATTGAGAAGGCAGTTAAGATTTTTGTATAGGCTCTCAGGATGGCTCCATGAGAGGGCCT
GCATTGCTTGCAGAAATCCCAAAGCACTCAAAGCAAAGAAAGGAGACAGAAATAAAGCATTTAAGGAAGGAAATTACAAG
CTAGCGTACGAACTGTACATGGGAGCCCTGGGGTAAACCCCAACAATATAAAAATAAATACTAAACTCTACTATAATCAG
GTTATGATTAATTCTAAGCTTAGGAAACTAGATAATGCAATACAAGACTGCACAAATACAGTGAAGCTCAATGACACCTA
TTTAAAAGCCTACTTGAGAAGAGTTCAGTGTTACATGAACATGAAACAGTATGAAGAAGCAGTGCACAATTATGAAAAAG
TGTATCAGATAGAGAAAACAAAAAAACACAAACAACTCCTAAAAAATGCACAGCTGAAACTGAAGAAGGGTAAGAAGAAA
GATTACTACAAGATTCTGGGAGTGGACAAGAATGCCTCTGAGGACAAGATCAAGACAGCTTATCACAAATGGGCCTTAAT
GCACCATCCAGATTGGCACAGTGGAGGCAGTGCTGAAGTTCAGAAGGAGGAGGGGAGGTTCAAAGAAATTGGAGAGGCCT
TTACCATCTTCTCTGATCCCAAGAAAAAGACTCTCCAGGAGAGTGGCCAAGACCTGGACAAGGAGGGCATGAATATGGGT
GATTTTGATGCAAATAGTATCTTCAAGGCATTCTTCAGTGGTCTTGGGGCTTCAGCTTTGAAGCGTCTGGTCCAGGGAAT
TTTTTT

Alignment

ORF - retro_mmul_501 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.84 %
• Parental protein coverage: 93.12 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  FKEQGNAYYAKKDYNEAYNYYTKAIDMCPKNASYYGNRAATLMMLGRFREALGDAQQSVRLDDSFVRGHL
          FKEQGNAYY.KKDYNEAYNY.TKA...CPKN.SYY.N.AATL.MLGRF.EALGDA.QS.RLDDSFV.GHL
Retrocopy FKEQGNAYYVKKDYNEAYNY-TKALGICPKNTSYYSNQAATLIMLGRFQEALGDAHQSLRLDDSFVQGHL

Parental  REGKCHLSLGNAMAACRSFQRALELDHKNAQAQQEFKNANAVMEYEKIAETDFEKRDFRKVVFCMDRALE
          .EGKC.LS.........SFQRALELDHKNAQ..QEFKNAN..MEYEK.A.TDFEK.D.RKVV.CMD.AL.
Retrocopy GEGKCPLSP*RMPWPYVSFQRALELDHKNAQE*QEFKNANSIMEYEKLAKTDFEKHDIRKVVLCMDCALL

Parental  FAPACHRFKILKAECLAMLGR-YPEAQSVASDILRMDSTNADALYVRGLCLYYEDCIEKAVQFFVQALRM
          .APACH.FKILKAE.L.MLG..YPEAQSVASDIL.M.STNAD.LYV.GLCLYYEDCIEKAV..FV.ALRM
Retrocopy LAPACHCFKILKAEYLVMLGH<YPEAQSVASDILQMESTNADPLYV*GLCLYYEDCIEKAVKIFV*ALRM

Parental  APDHEKACIACRNAKALKAK-KEDGNKAFKEGNYKLAYELYTEAL-GIDPNNIKTNAKLYCNRGTVNSKL
          AP.....C...........K.K.D.NKAFKEGNYKLAYELY..AL.G..PNNIK.N.KLY.N....NSKL
Retrocopy AP*EGLHCL--QKSQSTQSK>KGDRNKAFKEGNYKLAYELYMGAL<GVNPNNIKINTKLYYNQVMINSKL

Parental  RKLDDAIEDCTNAVKLDDTYIKAYLRRAQCYMDTEQYEEAVRDYEKVYQTEKTKEHKQLLKNAQLELKKS
          RKLD.AI.DCTN.VKL.DTY.KAYLRR.QCYM...QYEEAV..YEKVYQ.E...........AQL.LKK.
Retrocopy RKLDNAIQDCTNTVKLNDTYLKAYLRRVQCYMNMKQYEEAVHNYEKVYQIEXXXXXXXXXXXAQLKLKKG

Parental  KRKDYYKILGVDKNASEDEIKKAYRKRALMHHPDRHSGASAEVQKEEEKKFKEVGEAFTILSDPKKKTRY
          K.KDYYKILGVDKNASED.IK.AY.K.ALMHHPD.HSG.SAEVQK.EE..FKE.GEAFTI.SDPKKKT..
Retrocopy KKKDYYKILGVDKNASEDKIKTAYHKWALMHHPDWHSGGSAEVQK-EEGRFKEIGEAFTIFSDPKKKTLQ

Parental  DSGQDLDEEGMNMGDFDPNNIFKAFFGGPG-GFSFEASGPGSFF
          .SGQDLD.EGMNMGDFD.N.IFKAFF.G.G.GFSFEASGPG.FF
Retrocopy ESGQDLDKEGMNMGDFDANSIFKAFFSGLG<GFSFEASGPGNFF

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	0.11 RPM	46.28 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	57.67 RPM
SRP007412_cerebellum	0.06 RPM	35.26 RPM
SRP007412_heart	0.00 RPM	17.19 RPM
SRP007412_kidney	0.00 RPM	20.66 RPM
SRP007412_liver	0.00 RPM	4.95 RPM
SRP007412_testis	0.00 RPM	30.76 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_501 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_501 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_501 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_398
Pan troglodytes	retro_ptro_304
Pongo abelii	retro_pabe_317

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015749	1 retrocopy	retro_cfam_451,
Callithrix jacchus	ENSCJAG00000035699	2 retrocopies	retro_cjac_2381, retro_cjac_2475,
Homo sapiens	ENSG00000168259	1 retrocopy	retro_hsap_3524,
Gorilla gorilla	ENSGGOG00000010230	2 retrocopies	retro_ggor_2382, retro_ggor_396,
Myotis lucifugus	ENSMLUG00000011968	2 retrocopies	retro_mluc_1232, retro_mluc_1527,
Macaca mulatta	ENSMMUG00000016118	3 retrocopies	retro_mmul_1084, retro_mmul_1854, retro_mmul_501 ,
Nomascus leucogenys	ENSNLEG00000011230	2 retrocopies	retro_nleu_1569, retro_nleu_490,
Pongo abelii	ENSPPYG00000008402	2 retrocopies	retro_pabe_2911, retro_pabe_317,
Pan troglodytes	ENSPTRG00000009188	2 retrocopies	retro_ptro_2393, retro_ptro_304,