RetrogeneDB ID: retro_mmul_963

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 12:72882664..72883673(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.5357
• Ensembl ID: ENSMMUG00000004696
• Aliases: None
• Description: heat shock cognate 71 kDa protein [Source:RefSeq peptide;Acc:NP_001248586]

Sequence

>retro_mmul_963
CAAGCTACCAAACATCCTGGAACCATTGCTGGTCTCAATGTACTTAAAATTTTCAAAGAACCAGCTGCTGCTTCTGTTGC
TTATGGTGCAGACATAAAGGTTGGAGCTGAAAGAAGTGTGCTCATCTATGACTTAAGAAATGAAATGTTTGACGTGTCTG
TCCTCACTCTTGAGAATGAAATATTTGAGATCAAATCTATAGCTGGAAATACCCACTTAGGTGGAGAAGATTTTTGACAA
CCAAATGATCAAACATTTTATTGCTGAGTTCAAATGCAAGCATAAGGACAGTAGTGAGAACAACAGGGCTGTGTGATGCT
TCTGTACTGCTTGTGATGGGCTAATTGCATTCTCCCTTCCAGCACCCAGGCCAGTATTGAGATGGATTCTCTCTGTGAAG
GAACAGATATGTATACCTCCATTACTCATGCCCATTTGAAGAACTGAATGCTGTCCTGTTCCATGGCACCCAGGACCCGA
TAGAGATAGCCCTTCAGGACACCAAACTAGAAAAATTGCAGATTCATGTTATTGTCCTGGTAAGTGGTTCCATCTGTATC
TCCTAGATCCAAAAGCTTCCTCAATAATTATTTAGTGGAAAAGAACTGAGCAAGAGCATTGACCCTGATGAAGCTGTTGC
TTACGGTGCAGCTGTCCAGGCAGCCATCCTATCTTAAGACAAATCTTAAACTGTTCAAGGTTTGCTACTTTTGGATTTAC
TCCTCTTCTCTTTGGTAATGATGCTGCTGTAGAGTCATGACTGTTCCCACGAAATGCAATATACTTTTCTTACCAAGCAG
ACCCAGACCTTCACTACCTATCCTGACAACCAACCCGTATGCTCATTCAAGCTTTTGAAGGTGAGAGTGCCATAACCAAG
GATAACAATTTGCTAGTTATCCAGGACAAGTTTGAGCTCACAGGCATACTTCCTGCTCCCTTTGCTGTGCCTCAAATTAA
AGTCACTTGTAATATTGATGTCAATGTCATCCTCAACATCTCCTTGGTA

Alignment

ORF - retro_mmul_963 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.34 %
• Parental protein coverage: 52.01 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  QATKDAGTIAGLNVLRIINEPTAAAIAYGLDKKVGAERNVLIFDLGGGTFDVSILTIEDGIFEVKSTAGD
          QATK..GTIAGLNVL.I..EP.AA..AYG.D.KVGAER.VLI.DL....FDVS.LT.E..IFE.KS.AG.
Retrocopy QATKHPGTIAGLNVLKIFKEPAAASVAYGADIKVGAERSVLIYDLRNEMFDVSVLTLENEIFEIKSIAGN

Parental  THLGGEDF-DNRMVNHFIAEFKRKHKKDISENKRAVRRLRTACER-AKRTLSSSTQASIEIDSLYEGIDF
          THLGGEDF.DN.M..HFIAEFK.KHK.D.SEN.RAV....TAC...A...L.SSTQASIE.DSL.EG.D.
Retrocopy THLGGEDF>DNQMIKHFIAEFKCKHK-DSSENNRAV*CFCTACDG<ANCILPSSTQASIEMDSLCEGTDM

Parental  YTSITRAR-FEELNADLFRGTLDPVEKALRDAKLDKSQIHDIVLVGGSTRIPKIQKLLQDFFNGKELNKS
          YTSIT.A..FEELNA.LF.GT.DP.E.AL.D.KL.K.QIH.IVLV.GS..I..IQKL.Q..F.GKEL.KS
Retrocopy YTSITHAH<FEELNAVLFHGTQDPIEIALQDTKLEKLQIHVIVLVSGSICIS*IQKLPQ*LFSGKELSKS

Parental  INPDEAVAYGAAVQAAILSGDKSENVQDLLLLDV-TPLSLGIETA-GGVMTVLIKRNT-TIPTKQTQTFT
          I.PDEAVAYGAAVQAAILS.DKS..VQ.LLLLD..TPL..G...A...VMTV..K.N..T..TKQTQTFT
Retrocopy IDPDEAVAYGAAVQAAILS*DKS*TVQGLLLLDL<TPLLFGNDAA<CRVMTVPTKCNI<TFLTKQTQTFT

Parental  TYSDNQP-GVLIQVYEGERAMTKDNNLL---GKFELTGIPPAPRGVPQIEVTFDIDANGILNVSAV
          TY.DNQP...LIQ..EGE.A.TKDNNLL....KFELTGI.PAP..VPQI.VT..ID.N.ILN.S.V
Retrocopy TYPDNQP<RMLIQAFEGESAITKDNNLLVIQDKFELTGILPAPFAVPQIKVTCNIDVNVILNISLV

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	1399.06 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	1177.02 RPM
SRP007412_cerebellum	0.00 RPM	1090.15 RPM
SRP007412_heart	0.00 RPM	748.79 RPM
SRP007412_kidney	0.00 RPM	1404.90 RPM
SRP007412_liver	0.00 RPM	789.22 RPM
SRP007412_testis	0.08 RPM	185.00 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_963 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_963 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_963 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2384
Pan troglodytes	retro_ptro_1743
Gorilla gorilla	retro_ggor_1810

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Parental genes homology:

Parental genes homology involve 27 parental genes, and 74 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000004884	2 retrocopies	retro_acar_21, retro_acar_6,
Ailuropoda melanoleuca	ENSAMEG00000008425	1 retrocopy	retro_amel_126,
Anas platyrhynchos	ENSAPLG00000010667	1 retrocopy	retro_apla_6,
Bos taurus	ENSBTAG00000013162	1 retrocopy	retro_btau_354,
Canis familiaris	ENSCAFG00000011666	3 retrocopies	retro_cfam_140, retro_cfam_191, retro_cfam_509,
Ciona intestinalis	ENSCING00000009665	1 retrocopy	retro_cint_12,
Cavia porcellus	ENSCPOG00000004169	3 retrocopies	retro_cpor_1072, retro_cpor_619, retro_cpor_938,
Ciona savignyi	ENSCSAVG00000008588	1 retrocopy	retro_csav_3,
Dipodomys ordii	ENSDORG00000015467	1 retrocopy	retro_dord_16,
Echinops telfairi	ENSETEG00000010996	1 retrocopy	retro_etel_43,
Ficedula albicollis	ENSFALG00000005812	1 retrocopy	retro_falb_18,
Felis catus	ENSFCAG00000001132	6 retrocopies	retro_fcat_132, retro_fcat_1331, retro_fcat_1571, retro_fcat_1775, retro_fcat_556, retro_fcat_79,
Homo sapiens	ENSG00000109971	8 retrocopies	retro_hsap_2384, retro_hsap_2710, retro_hsap_2758, retro_hsap_340, retro_hsap_3698, retro_hsap_4892, retro_hsap_4896, retro_hsap_68,
Gallus gallus	ENSGALG00000006512	1 retrocopy	retro_ggal_8,
Loxodonta africana	ENSLAFG00000030312	4 retrocopies	retro_lafr_1218, retro_lafr_391, retro_lafr_790, retro_lafr_797,
Meleagris gallopavo	ENSMGAG00000001929	1 retrocopy	retro_mgal_9,
Myotis lucifugus	ENSMLUG00000004834	3 retrocopies	retro_mluc_1800, retro_mluc_2300, retro_mluc_777,
Macaca mulatta	ENSMMUG00000004696	7 retrocopies	retro_mmul_1536, retro_mmul_2188, retro_mmul_2628, retro_mmul_2632, retro_mmul_580, retro_mmul_778, retro_mmul_963 ,
Monodelphis domestica	ENSMODG00000012958	2 retrocopies	retro_mdom_127, retro_mdom_99,
Mustela putorius furo	ENSMPUG00000005810	9 retrocopies	retro_mputfur_1048, retro_mputfur_1056, retro_mputfur_1144, retro_mputfur_131, retro_mputfur_188, retro_mputfur_309, retro_mputfur_627, retro_mputfur_694, retro_mputfur_958,
Oreochromis niloticus	ENSONIG00000004759	1 retrocopy	retro_onil_2,
Pelodiscus sinensis	ENSPSIG00000012450	2 retrocopies	retro_psin_17, retro_psin_5,
Pan troglodytes	ENSPTRG00000004404	5 retrocopies	retro_ptro_1743, retro_ptro_2507, retro_ptro_272, retro_ptro_3259, retro_ptro_3264,
Taeniopygia guttata	ENSTGUG00000000491	1 retrocopy	retro_tgut_7,
Takifugu rubripes	ENSTRUG00000005265	1 retrocopy	retro_trub_30,
Tursiops truncatus	ENSTTRG00000011139	6 retrocopies	retro_ttru_1507, retro_ttru_1650, retro_ttru_1696, retro_ttru_35, retro_ttru_741, retro_ttru_808,
Xiphophorus maculatus	ENSXMAG00000001602	1 retrocopy	retro_xmac_20,