RetrogeneDB ID: retro_mmul_1085

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 14:113047650..113048925(+)
• Located in intron of: ENSMMUG00000012267

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.10126
• Ensembl ID: ENSMMUG00000009948
• Aliases: None
• Description: Histone deacetylase [Source:UniProtKB/TrEMBL;Acc:F6RIU8]

Sequence

>retro_mmul_1085
CCTCACAAAGCCAATGCTGAGGAGATGACCAAGTACCACAGTGATTACTGCATTAAATTATTGTGCTCCATCTGTCCAGA
TTACGTGTCCAAGCACAGCAAGCAGATGCGGGGATTTAATGTTAGTGAGGACTGTCCAGTATCTGATGGCCTGTTTGACT
TCTGTCAGTTGTCTACTGGTGGCTCTGTGGCAAGTGCTGTGAAACTTAATAAGCAGCAGATGGACATTGCTGTGAATTGG
GCTGGGGGCCTGCACCATGCAAAGAAGTTCAAGGCATCTGGCTTCTGTTATATCAGTGATACAATCTGGGCCACCCTGGA
ACTGCTAAAGTATCACCAGAGGGTGTTGTATGTTGATGTTGATATTCACCATGATGATGGCATGGAAGAGACCTTCTATA
TTACAGGCCAGGTCAGGACTGTGTCCTTTCATAAATATGGAGAGTACTTCCCAGGAAATGGGGACCTATGGGATATTGGG
ACTGGCAAGGCAGATATTATGCTGTTAACTGTCTGCTCCTAGATGGGATTGATTATGAGTCCTGTGAGGCCATTTTGAAA
CTGGTCATGTCCAAAGTAATAGAGATGCTCCTGTCTAGCGTGATGGTCTTATGGCATGTCTCAGATGCCTTGTTTAGGGA
TCAGTTAGATTGCTTTAATCTGACCATGAAAGCGCATGCCAAGTGTATGGAATTTGTCAAGAGCTTCAACCTGCCTATAC
TGTTGATGGCAGAAGGTGGTTACACCATTTATAACGTTGCTCAGTGCTGGAAATAAGAAATAGCTGTGGCTCTGGATATG
GAGACTTCTAATGAGCCTTCATACAATGACTAGTTTGAATACTTCAGACCATATTTCAAGCCCTACATCAGTCCTTCCAA
TATGACTAACTAGAACACTAATGAGTACCTGGAGAAGATTAAATAATGGCTGTTTGAGAACCTAGTGATGCAGCCCCATC
CATCTGCAGTCCAAATGCAGGTGATTCCTGAGGATGCTGTCCCTCAAGAGGGTGGCATTGAGAATGAAGAAGACCCTGAC
AAGCATCTCCATCTGTTTCTCTGACAGACGAATTACCTGTGAGGAAGAGTTCTTCGGTTCTGATGAGGAGGGAGAGGGTG
GCCGCAAGATCTCTCCCATCTTCAGAAAATCCAAGAGGGTTAAAACAGGATGAAAAAGAGAGACTCAGAGATGAAGAAAG
AAGTCACAGAAGCGGAGAAAAACAAAGGAGAAGAAGCCAGGAGCCAAAGAGGTCAAGGACCAGGTCAAGCTGGCC

Alignment

ORF - retro_mmul_1085 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.76 %
• Parental protein coverage: 99.77 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PHKANAEEMTKYHSDDYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVASAVKLN
          PHKANAEEMTKYHSD..IK.L.SI.PD..S..SKQM..FNV.EDCPV.DGLF.FCQLSTGGSVASAVKLN
Retrocopy PHKANAEEMTKYHSDYCIKLLCSICPDYVSKHSKQMRGFNVSEDCPVSDGLFDFCQLSTGGSVASAVKLN

Parental  KQQTDIAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMT
          KQQ.DIAVNWAGGLHHAKK..ASGFCY..D...A.LELLKYHQRVLY.D.DIHH.DG.EE.FY.T..V.T
Retrocopy KQQMDIAVNWAGGLHHAKKFKASGFCYISDTIWATLELLKYHQRVLYVDVDIHHDDGMEETFYITGQVRT

Parental  VSFHKYGEYFPGTGDLRDIGAGK-GKYYAVNYPLRDGIDDESYEAIFKPVMSKVMEMFQPSAVVLQCGSD
          VSFHKYGEYFPG.GDL.DIG.GK.G.YYAVN..L.DGID.ES.EAI.K.VMSKV.EM...S..VL...SD
Retrocopy VSFHKYGEYFPGNGDLWDIGTGK<GRYYAVNCLLLDGIDYESCEAILKLVMSKVIEMLLSSVMVLWHVSD

Parental  SLSGDRLGCFNLTIKGHAKCVEFVKSFNLPMLMLGGGGYTIRNVARCWTYETAVALDTEIPNELPYNDYF
          .L..D.L.CFNLT.K.HAKC.EFVKSFNLP.L....GGYTI.NVA.CW..E.AVALD.E..NE..YND.F
Retrocopy ALFRDQLDCFNLTMKAHAKCMEFVKSFNLPILLMAEGGYTIYNVAQCWK*EIAVALDMETSNEPSYND*F

Parental  EYFGPDFKLHISPSNMTNQNTNEYLEKIKQRLFENLRMLPHAPGVQMQAIPEDAIPEESGDEDEEDPDKR
          EYF.P.FK..ISPSNMTN.NTNEYLEKIK..LFENL.M.PH...VQMQ.IPEDA.P.E.G....E.....
Retrocopy EYFRPYFKPYISPSNMTN*NTNEYLEKIK*WLFENLVMQPHPSAVQMQVIPEDAVPQE-GGIENEEDPDK

Parental  -ISICSSDKRIACEEEFSDSEEEGEGGRKNSSNFKKAKRVKTEDEKEKDPEEKKEVTEEEKTKEEKPEAK
          .ISIC.SD.RI.CEEEF..S.EEGEGGRK.S..F.K.KRVKT....E.....KK......KTKE.KP.AK
Retrocopy >ISICFSDRRITCEEEFFGSDEEGEGGRKISPIFRKSKRVKTG*KRETQR*RKKS-QKRRKTKEKKPGAK

Parental  GVKEEVKLA
          .VK..VKLA
Retrocopy EVKDQVKLA

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	7.62 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	7.54 RPM
SRP007412_cerebellum	0.00 RPM	5.10 RPM
SRP007412_heart	0.00 RPM	12.37 RPM
SRP007412_kidney	0.00 RPM	34.86 RPM
SRP007412_liver	0.00 RPM	24.34 RPM
SRP007412_testis	0.15 RPM	83.64 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1085 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1085 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1085 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_826
Gorilla gorilla	retro_ggor_676

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona intestinalis	ENSCING00000002649	1 retrocopy	retro_cint_18,
Callithrix jacchus	ENSCJAG00000000970	2 retrocopies	retro_cjac_2490, retro_cjac_830,
Homo sapiens	ENSG00000116478	1 retrocopy	retro_hsap_826,
Gorilla gorilla	ENSGGOG00000011741	1 retrocopy	retro_ggor_676,
Myotis lucifugus	ENSMLUG00000013837	1 retrocopy	retro_mluc_283,
Macaca mulatta	ENSMMUG00000009948	2 retrocopies	retro_mmul_1085 , retro_mmul_2518,
Macaca mulatta	ENSMMUG00000012588	1 retrocopy	retro_mmul_49,
Mus musculus	ENSMUSG00000028800	1 retrocopy	retro_mmus_153,
Nomascus leucogenys	ENSNLEG00000002473	1 retrocopy	retro_nleu_259,
Otolemur garnettii	ENSOGAG00000005709	3 retrocopies	retro_ogar_2181, retro_ogar_3022, retro_ogar_3313,
Pelodiscus sinensis	ENSPSIG00000004134	1 retrocopy	retro_psin_44,
Pteropus vampyrus	ENSPVAG00000013325	1 retrocopy	retro_pvam_1339,
Rattus norvegicus	ENSRNOG00000009568	3 retrocopies	retro_rnor_1091, retro_rnor_1098, retro_rnor_2457,
Sarcophilus harrisii	ENSSHAG00000008787	1 retrocopy	retro_shar_573,
Tursiops truncatus	ENSTTRG00000001613	1 retrocopy	retro_ttru_1236,