RetrogeneDB ID: retro_mmul_2518

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:92017077..92018359(+)
• Located in intron of: None

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_2518
CGCCCTCACAAAGCCAATGCTGAGGAGATGACCAAGTACCATAGTGACGACTACATTAAATTCCTGCGCTCCATCCGTCC
AGATAACATGTCGGAGTACAGCAAGCAGATGCAGAGATTCAACCTTGGTGAGGACTGTCCAGTATTCAACGGCCTATTTG
AGTTCTGTCAGTTGTCTACCGGTGGTTCTGTGGCAAGTGCTGTGAAACTTAATAAGCAGCAGACGGACATGGCTGTGAAT
TGGGCTGGGGGCCTGCACCATGCAAAGAAGTCTGAGGCATCTGGCTTCTGTTACGTCAATAATACCGTCTTGGCCATTCT
GGAACTGCTAAAGCATCACCAGAGGGTGCTGTATATTGACATTGATGTTCACCATAGCGACGGCATGGAAGAGGCCTTCT
ATACCACAGACCGGGTCATGACTGTGTCCTTTCATAAGTATGGAGAGTACTTCCCAGGAACTGGGGACCTGTGGGATATC
GGGGCTGGCAAAGGCAAGTATTATGCTGTTAACTACCCGCTCCAAGACGGGATTGATGACAAGTCCTATGAGGCCATTTT
CAAGCCAGTCATGTCCAAAGTAATGGAGATGTTCCAGCCTAGCTCAGTGGTCTTACAGTGTGGCTCAGACTCCCTGTCTG
GGGATCGGTTAGGTTGCTTCAATCTAACCATCAAAGGGCACGCCAAGTGTGTGGAATTTGTCAAGAGCTTTAACCTGCCT
ATGCTGATGCTGGGAGGTGGTGATTACACCATTTGTAATGTTGCCCGGTGCTGGACATACGAGACAGCTGTGGCCCTGGA
TACGGAGATCCCTAATGAGCTTCCGTACAATGACTACTTTGAATACTTTGGACCAGATTTCAAGCTCCACATCAGTCCTT
CCAATATGACTAACCAGAACACGAATGAGTACCTGGAGAAGATCGAACAGCGACTGTTTGAGAACCTTAGAATGCTGCTG
CATGCACCTAGGGTCCAAATGCAGGCAATTCCTGAAGACGCCATCCCTGAGGAGAGTGGCGATGAGGACGAAGAAGACCC
TGATAAGCGCATCTCGATCTGCTCCTCCGACAAACGAATTGCCTGTGAGGAAGTTCTCCAATTCTGAAGAGGAAGGAGAG
GGGGGCCGCAAGAACTCTTCCAACTTCAAAAAAGCCAAGAGAGTCAAAACAGAGGATGAAAAAGAGAAAGACCCAGAGGA
GAAGAAAGAAGCCACAGAAGAGGAGAAAACCAAGGAGGAAAAGCCAGAAGCCAAAGGGGTCAAGGAGGAGGTCAAGTTGG
CC

Alignment

ORF - retro_mmul_2518 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.74 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RPHKANAEEMTKYHSDDYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVASAVKL
          RPHKANAEEMTKYHSDDYIKFLRSIRPDNMSEYSKQMQRFN.GEDCPVF.GLFEFCQLSTGGSVASAVKL
Retrocopy RPHKANAEEMTKYHSDDYIKFLRSIRPDNMSEYSKQMQRFNLGEDCPVFNGLFEFCQLSTGGSVASAVKL

Parental  NKQQTDIAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVM
          NKQQTD.AVNWAGGLHHAKKSEASGFCYVN..VLAILELLK.HQRVLYIDID.HH.DG.EEAFYTTDRVM
Retrocopy NKQQTDMAVNWAGGLHHAKKSEASGFCYVNNTVLAILELLKHHQRVLYIDIDVHHSDGMEEAFYTTDRVM

Parental  TVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNYPLRDGIDDESYEAIFKPVMSKVMEMFQPSAVVLQCGSD
          TVSFHKYGEYFPGTGDL.DIGAGKGKYYAVNYPL.DGIDD.SYEAIFKPVMSKVMEMFQPS.VVLQCGSD
Retrocopy TVSFHKYGEYFPGTGDLWDIGAGKGKYYAVNYPLQDGIDDKSYEAIFKPVMSKVMEMFQPSSVVLQCGSD

Parental  SLSGDRLGCFNLTIKGHAKCVEFVKSFNLPMLMLGGGGYTIRNVARCWTYETAVALDTEIPNELPYNDYF
          SLSGDRLGCFNLTIKGHAKCVEFVKSFNLPMLMLGGG.YTI.NVARCWTYETAVALDTEIPNELPYNDYF
Retrocopy SLSGDRLGCFNLTIKGHAKCVEFVKSFNLPMLMLGGGDYTICNVARCWTYETAVALDTEIPNELPYNDYF

Parental  EYFGPDFKLHISPSNMTNQNTNEYLEKIKQRLFENLRMLPHAPGVQMQAIPEDAIPEESGDEDEEDPDKR
          EYFGPDFKLHISPSNMTNQNTNEYLEKI.QRLFENLRML.HAP.VQMQAIPEDAIPEESGDEDEEDPDKR
Retrocopy EYFGPDFKLHISPSNMTNQNTNEYLEKIEQRLFENLRMLLHAPRVQMQAIPEDAIPEESGDEDEEDPDKR

Parental  ISICSSDKRIACEEEF-SDSEEEGEGGRKNSSNFKKAKRVKTEDEKEKDPEEKKEVTEEEKTKEEKPEAK
          ISICSSDKRIACEE......EE.GEGGRKNSSNFKKAKRVKTE...................KEEKPEAK
Retrocopy ISICSSDKRIACEEVL>NSEEE-GEGGRKNSSNFKKAKRVKTEXXXXXXXXXXXXXXXXXXXKEEKPEAK

Parental  GVKEEVKLA
          GVKEEVKLA
Retrocopy GVKEEVKLA

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	0.45 RPM	7.62 RPM
SRP007412_brain_prefrontal_cortex	0.48 RPM	7.54 RPM
SRP007412_cerebellum	0.19 RPM	5.10 RPM
SRP007412_heart	0.41 RPM	12.37 RPM
SRP007412_kidney	1.88 RPM	34.86 RPM
SRP007412_liver	0.67 RPM	24.34 RPM
SRP007412_testis	6.22 RPM	83.64 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2518 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2518 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2518 has 0 orthologous retrocopies within eutheria group .

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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,