RetrogeneDB ID: retro_mmul_1322

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 17:80403005..80403924(-)
• Located in intron of: ENSMMUG00000030642

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.1334
• Ensembl ID: ENSMMUG00000007046
• Aliases: None
• Description: adiponectin receptor protein 1 [Source:RefSeq peptide;Acc:NP_001248104]

Sequence

>retro_mmul_1322
ATGTCTTCCCACAAAGGATCTGTGGTGGCATGGGGCAATGCGGCTCCTGCCAGTAACAGGGAAACTGACATGGTGGAACT
AGCTGAACTGGGACCCCTACTACAAGAGAAGGATGGATGGGTTATCACCAACCCAACCAAAGCTGAAGAAGTGCAAACAT
GTCCAATGCCTCAGGAAAAGGAGGAGAAGGTAAAGCTACTGATGCACTGCACTTCCACTATGCCACGGAGGAGATGGAGG
AGTTTGTGTGCAAGGTCTGGGAGGGACACTGGAGGGCCATCCCATATGATGTTGTCCCTGACTGACTGAAGGACAATGAC
TACCTGCTACATGGCCATAGACCATCCATGCCTTCCTTTTGGGCTTGCTTCAAGAGCATCTTCCACATCCATGTGAAAAC
GGGCATCATCTGGACCCATCTGCTTGGTTTCATGCTGTTTCTCTTTTGAGGATCTTGACCATGCTCAGACCAAATATGTA
CTTCATGGACCCTCTACAGGAGAAAGTGGTATGGGGACGTCCTTTGTGAGTGTAGTGCTCTGCCTCAGTTCCTCCTGGCT
ATTCCACACTGTCTATTGTCATTCAGAGTAAGTCTCTTAGACTTTTTCCAAACTGAACTACTCAGCGATTGCTCTACTGA
TTACGGGGAGCTTTGTCCCCTGCTCTGTTACTCCTTCCACTGTTCCCCACAGCCAAGCTCATCTGCCTCTTCTTTGTCTG
TGTTCTGGGCATTTCTGCCATCACGGTGGCACAGTGGGACCAGTTTCCACTCCTAAGCACCAGCAGACACAGCAGGAGCA
TTCCTGGGACTTGGCTTGAGTGTTATTGTGCCCGTCATGCATTTTCCTATCACTAAAGCTTTGTCAGGGCCAGCGCCATG
GGCTGGATGGGCTGGTCCTTCCTCACAGCTGTGATGTAC

Alignment

ORF - retro_mmul_1322 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.27 %
• Parental protein coverage: 82.67 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 8

Retrocopy - Parental Gene Alignment:

Parental  MSSHKGSVVAQGNGTPASNRETDTVELAELGPLLEEKGKRVIANPTKAEEEQTCPVPQEEEEEVRVLTL-
          MSSHKGSVVA.GN..PASNRETD.VELAELGPLL.EK...VI.NPTKAEE.QTCP.PQE..EE...L...
Retrocopy MSSHKGSVVAWGNAAPASNRETDMVELAELGPLLQEKDGWVITNPTKAEEVQTCPMPQE-KEEKVKLLM<

Parental  PLQAHHAMEKMEEFVYKVWEGRWRVIPYDVLPDWLKDNDYLLHGHRPPMPSFRACFKSIFRIHTETGNIW
          .L..H.A.E.MEEFV.KVWEG.WR.IPYDV.PD.LKDNDYLLHGHRP.MPSF.ACFKSIF.IH..TG.IW
Retrocopy ALHFHYATEEMEEFVCKVWEGHWRAIPYDVVPD*LKDNDYLLHGHRPSMPSFWACFKSIFHIHVKTGIIW

Parental  THLLGFVLFLF-LGILTMLRPNMYFMAPLQEKVVF-GMFFLGAVLCLSFSWLFHTVYCHSEKVSRTFSKL
          THLLGF.LFLF.L.ILTMLRPNMYFM.PLQEKVV..G..F...VLCLS.SWLFHTVYCHSE.VS.TFSKL
Retrocopy THLLGFMLFLF<LRILTMLRPNMYFMDPLQEKVVW<GTSFVSVVLCLSSSWLFHTVYCHSE*VS*TFSKL

Parental  DYSGIALLIMGSFV-PWLYYSFYCSPQP-RLIYLSIVCVLGISAIIVAQWDRF-ATPKHRQTR-AGVFLG
          .YS.IALLI.GSFV.P.L.YSF.CSPQP..LI.L..VCVLGISAI.VAQWD.F..TPKH.QT..AG.FLG
Retrocopy NYSAIALLITGSFV<PLLCYSFHCSPQP<KLICLFFVCVLGISAITVAQWDQF<STPKHQQTQ<AGAFLG

Parental  LGLSGVVPTMHFTIAE-GFVKATTVGQMGWFFLMAVMY
          LGLS..VP.MHF.I....FV.A...G.MGW.FL.AVMY
Retrocopy LGLSVIVPVMHFPITK<SFVRASAMGWMGWSFLTAVMY

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	58.04 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	75.44 RPM
SRP007412_cerebellum	0.13 RPM	52.95 RPM
SRP007412_heart	0.00 RPM	80.44 RPM
SRP007412_kidney	0.00 RPM	96.83 RPM
SRP007412_liver	0.00 RPM	76.20 RPM
SRP007412_testis	0.23 RPM	75.50 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1322 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1322 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1322 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_1072
Callithrix jacchus	retro_cjac_504

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012199	1 retrocopy	retro_amel_1853,
Choloepus hoffmanni	ENSCHOG00000006450	8 retrocopies	retro_chof_1127, retro_chof_1222, retro_chof_1917, retro_chof_2218, retro_chof_2380, retro_chof_471, retro_chof_749, retro_chof_995,
Callithrix jacchus	ENSCJAG00000006268	3 retrocopies	retro_cjac_2262, retro_cjac_740, retro_cjac_741,
Cavia porcellus	ENSCPOG00000000482	1 retrocopy	retro_cpor_470,
Dipodomys ordii	ENSDORG00000006876	1 retrocopy	retro_dord_19,
Felis catus	ENSFCAG00000013565	1 retrocopy	retro_fcat_1514,
Loxodonta africana	ENSLAFG00000003520	1 retrocopy	retro_lafr_277,
Macropus eugenii	ENSMEUG00000015439	1 retrocopy	retro_meug_516,
Microcebus murinus	ENSMICG00000007942	3 retrocopies	retro_mmur_1199, retro_mmur_184, retro_mmur_764,
Myotis lucifugus	ENSMLUG00000016102	2 retrocopies	retro_mluc_1275, retro_mluc_200,
Macaca mulatta	ENSMMUG00000007046	1 retrocopy	retro_mmul_1322 ,
Mustela putorius furo	ENSMPUG00000011215	1 retrocopy	retro_mputfur_550,
Otolemur garnettii	ENSOGAG00000033821	4 retrocopies	retro_ogar_1558, retro_ogar_1624, retro_ogar_2838, retro_ogar_783,
Ochotona princeps	ENSOPRG00000004528	3 retrocopies	retro_opri_101, retro_opri_1050, retro_opri_392,
Pongo abelii	ENSPPYG00000000342	1 retrocopy	retro_pabe_1072,
Sorex araneus	ENSSARG00000007680	1 retrocopy	retro_sara_25,
Ictidomys tridecemlineatus	ENSSTOG00000015459	3 retrocopies	retro_itri_215, retro_itri_257, retro_itri_512,
Tupaia belangeri	ENSTBEG00000015149	2 retrocopies	retro_tbel_1501, retro_tbel_1804,
Tarsius syrichta	ENSTSYG00000001491	1 retrocopy	retro_tsyr_125,
Tursiops truncatus	ENSTTRG00000006381	2 retrocopies	retro_ttru_1055, retro_ttru_863,