RetrogeneDB ID: retro_mmul_1645

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:166363685..166364488(+)
• Located in intron of: ENSMMUG00000004311

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.13490
• Ensembl ID: ENSMMUG00000020441
• Aliases: None
• Description: None

Sequence

>retro_mmul_1645
TTCCTTGATGAAGGTTTTACTGCCAAGGACATTCTGGACCAAAAATTTAATGAATTTTCTTCTGATGATGATTAGGATGG
CTTCTATGTCATGGACCTTAGAGACATTCTAAAGATATATCTAAGATGGTTAAAAACTCTTCCTCATGTCACCCCCTTTC
ATGGAGTCAAACATAATGATAGGAGAGCCATCATGAAGACTCTCACTGCCATTGGGACAGGATTTGACTGTGCTAGCAAG
GCTGAAATACAATTGGTGCAGATTCTGGGGATGCCCCCAAAAGAGGTTTATCTATGCAAATTCTTGTAAACAAATGTCTC
AAATTAAGTACACTGCCGATAATGGAGTCCAGATGATGATTTTCGGTAATAAGGTCAAGTTGATGTCAGTTGCCAGAACA
CACTCAAAGCAGAGTTGGTTTTTAAGATTGCAAATGATGATTCCAAAGCAGTCCGTCACCTCAGTGTTAAATCTGGTGCC
AAGCTCAAAGCCAGCAGGCTTCTTCTGGAATGGGCAAAAGAGCTAAATATTGATGTCACTGGTGTCAGCTTCCATGTAGG
AAGTAGCTGTACCAATCCTGAGACCTTTATGCAGGTAGTCTCCAATGTCCACTGTGTCTTTGACACAGGAGTTGAGTTTG
GTTTCAGTATGTAACTGCTTGATACTAGCAGTTGCTTTCCTGGATCTGAGGATGTGAGGCTTAAATCTGAAGTATTACCA
GTGTAATCAACCCAGCATAGGACAAGTATTTTCCACCAGACTCTAGAGTGAGAGTCACAGCTAAGCCAGGCAGATATTTC
ATG

Alignment

ORF - retro_mmul_1645 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.74 %
• Parental protein coverage: 58.13 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  FLDEGFTAKDILDQKINEVSFSDDKDAFYVADLGDILKKHLRWLKALPRVTPFYAVKCNDSKAIVKTLAA
          FLDEGFTAKDILDQK.NE.S..DD.D.FYV.DL.DILK..LRWLK.LP.VTPF..VK.ND..AI.KTL.A
Retrocopy FLDEGFTAKDILDQKFNEFSSDDD*DGFYVMDLRDILKIYLRWLKTLPHVTPFHGVKHNDRRAIMKTLTA

Parental  VGTGFDCASKTEIQLVQNLGVPP-ERIIYANPCKQVSQIKYAANNGVQMMTFDSEVELMKVTRAHP-KAK
          .GTGFDCASK.EIQLVQ.LG.PP..R.IYAN.CKQ.SQIKY.A.NGVQMM.F...V.LM.V.R.H..KA.
Retrocopy IGTGFDCASKAEIQLVQILGMPP>KRFIYANSCKQMSQIKYTADNGVQMMIFGNKVKLMSVARTHS<KAE

Parental  LVLRIATDDSKAVCRLSVKFGATLRNSRLLLERAKELNIDVVGVSFHVGSGCTDPETFVQAISDARCVFD
          LV..IA.DDSKAV..LSVK.GA.L..SRLLLE.AKELNIDV.GVSFHVGS.CT.PETF.Q..S...CVFD
Retrocopy LVFKIANDDSKAVRHLSVKSGAKLKASRLLLEWAKELNIDVTGVSFHVGSSCTNPETFMQVVSNVHCVFD

Parental  MGAEVGFSMYLLDIGGGFPGSEEVKLKFE-EITNVINPALDKYFPADSGVRIIAEPGRYYV
          .G.E.GFSM.LLD....FPGSE.V.LK.E..IT.VINPA.DKYFP.DS.VR..A.PGRY..
Retrocopy TGVEFGFSM*LLDTSSCFPGSEDVRLKSE<SITSVINPA*DKYFPPDSRVRVTAKPGRYFM

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	15.58 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	15.47 RPM
SRP007412_cerebellum	0.06 RPM	26.02 RPM
SRP007412_heart	0.00 RPM	36.57 RPM
SRP007412_kidney	0.23 RPM	80.51 RPM
SRP007412_liver	0.08 RPM	36.06 RPM
SRP007412_testis	0.04 RPM	182.10 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1645 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1645 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1645 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_3090
Callithrix jacchus	retro_cjac_3170

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 65 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011415	1 retrocopy	retro_amel_414,
Bos taurus	ENSBTAG00000004256	1 retrocopy	retro_btau_552,
Choloepus hoffmanni	ENSCHOG00000010898	2 retrocopies	retro_chof_1618, retro_chof_2111,
Callithrix jacchus	ENSCJAG00000006576	2 retrocopies	retro_cjac_3170, retro_cjac_3857,
Dasypus novemcinctus	ENSDNOG00000018474	31 retrocopies	retro_dnov_1032, retro_dnov_1128, retro_dnov_1129, retro_dnov_1137, retro_dnov_1212, retro_dnov_1235, retro_dnov_1418, retro_dnov_1434, retro_dnov_1493, retro_dnov_1594, retro_dnov_1595, retro_dnov_1677, retro_dnov_1778, retro_dnov_1810, retro_dnov_1813, retro_dnov_2016, retro_dnov_2027, retro_dnov_2108, retro_dnov_2147, retro_dnov_2180, retro_dnov_2212, retro_dnov_2461, retro_dnov_2551, retro_dnov_2564, retro_dnov_392, retro_dnov_740, retro_dnov_766, retro_dnov_781, retro_dnov_923, retro_dnov_943, retro_dnov_958,
Equus caballus	ENSECAG00000022690	2 retrocopies	retro_ecab_1002, retro_ecab_957,
Loxodonta africana	ENSLAFG00000005330	2 retrocopies	retro_lafr_218, retro_lafr_850,
Myotis lucifugus	ENSMLUG00000010423	1 retrocopy	retro_mluc_281,
Macaca mulatta	ENSMMUG00000020441	2 retrocopies	retro_mmul_157, retro_mmul_1645 ,
Monodelphis domestica	ENSMODG00000014779	1 retrocopy	retro_mdom_262,
Mustela putorius furo	ENSMPUG00000013321	1 retrocopy	retro_mputfur_1272,
Mus musculus	ENSMUSG00000011179	12 retrocopies	retro_mmus_2588, retro_mmus_2744, retro_mmus_2745, retro_mmus_2746, retro_mmus_2747, retro_mmus_2834, retro_mmus_2922, retro_mmus_3237, retro_mmus_3677, retro_mmus_503, retro_mmus_912, retro_mmus_984,
Nomascus leucogenys	ENSNLEG00000013820	1 retrocopy	retro_nleu_1119,
Pongo abelii	ENSPPYG00000012654	1 retrocopy	retro_pabe_3090,
Ictidomys tridecemlineatus	ENSSTOG00000000386	2 retrocopies	retro_itri_1751, retro_itri_801,
Tursiops truncatus	ENSTTRG00000004611	3 retrocopies	retro_ttru_1940, retro_ttru_731, retro_ttru_843,