RetrogeneDB ID: retro_mmul_1319

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 17:77289908..77291876(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.142
• Ensembl ID: ENSMMUG00000022686
• Aliases: None
• Description: None

Sequence

>retro_mmul_1319
ATGCCTGAGGAAGTGCACCATGAAGAGGAGGAGGTGGAGACTTTTGCCTTTCAGACAGAAATTGCCTAACTCAGGTCTCT
TATTATCAATATCTTCTATTCCAACAAGCAGATTTTCCTTCAAGAGTTGATTTCTAAAGTTTCTGATGCCTTGGACATGA
TTCTCTATGAGGGCCTGGCAGACACTTACAAGTTGGACAGTGGTAAAGAGCTGAAAATGGACATCATGCCCAACCCTCAG
GAATGTACCCTGACTTTGGTAGACACAGGCATTGGCATGACAAAGCTGATTTCATAAATACTTTGGGAACCATTGCCAAG
TCTGATACTAAAGGATTTATGGAGGCTCTTCAGGCTGGTGCAGACATCTCCATGATTGTCAATTTGGTGTTGGCTTTCAT
TCTGCCTATGTGGTGGCAGAGAAAGTGGTTGTGATCACAAAGCACAATGATGATGAACAGTGAACCTGGGAGTCCTCTGG
TGGGGGTTCCTTCACTGTATGTGCTGACCATGGCAGGGGTACCAAAATGATCCTCCACCTTAAAGAAAACCAGCAGAGTA
CTTAGAAGAGAGATGGGTCAAAGATGCAGTGAAAAAGCACTCACAGTTCATAGGCAAACCCATCACCCTCTATCTGAGGA
AGGGAAGAGAGAAGGAAATCAGTGATGATGAGGCAGGGGAAGAGAAAGGCAAGAAATAATAGGAGGATAAAGATAATGAG
GAAAAGCCCAAGATTGAAAATGTGGGTTCAAAGGAGGAGGATGACAGTGGCAAGGATAAGAAAAAGAAAACCAAGAAGAT
CAGAGATAAATACATTGATCAGGAAGAACTAAACAAGACCAAGCCTATTTGGACAAGAAACCATGATTACATCACCCAGG
AGAAGTATGGAGAATTCCGTAATAGCCACACTAATGACTGGGAAGACCACCTGGCAGTCAAGCACTTCTCTATAGAAGGT
CAGTTGGAATTCAGGGCATTGCTATTCATCGCCAGTCAGGCTCCTTTTGATTTCTTTGGGAATAATAAGAAAAAAGACAC
CATCAAACTCTACATCCTTCATGTGTTCATCGTGCACAGCTGTGATGAGCTGATACCAGAGGATCTCAACTTTATCCGTG
GTATGGTTGACTCTGAGGATCTACCCTTGAACATTTGAGAAATGCTCCAGCAGAGCAAAATCTTGAAAGCCATTCACGAA
AACATTGTTAAGTAGTACCTTGAGCTCTTCGCTGAGTTGGCAGAAGACAAAGAGAATTACAAGAAATCCTATGAGGTATT
CTCTGAAAATCTAAAATTTGGAATCCCCCAGGACGCCCCTAACTGGCAACACCTGTCTGAGCTGCTGCACTTTCACACCT
CCCAGTCTGGAGAAGAGATGACATCTCTGTCAGAATATGTCTTTTTTTTTTTTTATGAAGGATACACCTACTACATCACT
GGGGAGAGCAACGAACAGGTGGCCAGCTCTGCTTTCGTGGAGTGAGTGCAGAAGCGGGGCTTTAAGGTAGTGTATAATAC
CAACCCCACTGATAAGTACTGTATGCAGCAGCTCAAGGAGTTTAACGGGAAGGGCCTCATCTCAGTTACCAAGGAGGGTC
TGGAGCTACCTGAAGGTGAGGAGGAGAAGAAGAAAATGGAAGAGTGCAAAGTAAAGCTTGAGAACCTCTGCAAGTTCATG
AAAATAATCTTGGATAAGAAGGTTGACAAGGTGACAGTTTCCAATAGGCTTGAGTCTTCACTTGCTGCAATGTGACCAGC
ATCTATGGCTTGACAGCCATTATGGAGCAGATTGTGAAAGCCCAGGTACTTTGGGACACCTCTATGATGGTTACCTGATG
GCCAAAGGGCACCTGGTGATCACCATGACCACTGCATTGTGGAGACGCTGTGGCAGAAGGCTGAGGTGGACAACAATGAC
AAGGCTGTCAAGGACTGGGTGGTGCTGCTGTTGGAAACCAAGCTGCTC

Alignment

ORF - retro_mmul_1319 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.57 %
• Parental protein coverage: 90.46 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MPEEVHHGEEEVETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNASDALDKIRYESLTDPSKLDSGKE
          MPEEVHH.EEEVETFAFQ.EIA.L.SLIIN.FYSNK.IFL.ELIS..SDALD.I.YE.L.D..KLDSGKE
Retrocopy MPEEVHHEEEEVETFAFQTEIA*LRSLIINIFYSNKQIFLQELISKVSDALDMILYEGLADTYKLDSGKE

Parental  LKIDIIPNPQERTLTLVDTGIGMTK-ADLINNLGTIAKSGTKAFMEALQAGADISMIG-QFGVGFYSAYL
          LK.DI.PNPQE.TLTLVDTGIGMTK.AD.IN.LGTIAKS.TK.FMEALQAGADISMI..QFGVGF.SAY.
Retrocopy LKMDIMPNPQECTLTLVDTGIGMTK<ADFINTLGTIAKSDTKGFMEALQAGADISMIV<QFGVGFHSAYV

Parental  VAEKVVVITKHNDDEQYAWESSAGGSFTVRADHGEPIGRGTKVILHLKEDQ-TEYLEERRVKEVVKKHSQ
          VAEKVVVITKHNDDEQ..WESS.GGSFTV.ADH....GRGTK.ILHLKE.Q..EYLEER.VK..VKKHSQ
Retrocopy VAEKVVVITKHNDDEQ*TWESSGGGSFTVCADH----GRGTKMILHLKENQ<AEYLEERWVKDAVKKHSQ

Parental  FIGYPITLYLEKEREKEISDDEAEEEKGEKEEEDKDDEEKPKIEDVGSDEEDDSGKDKKKKTKKIKEKYI
          FIG.PITLYL.K.REKEISDDEA.EEKG.K..EDKD.EEKPKIE.VGS.EEDDSGKDKKKKTKKI..KYI
Retrocopy FIGKPITLYLRKGREKEISDDEAGEEKGKK**EDKDNEEKPKIENVGSKEEDDSGKDKKKKTKKIRDKYI

Parental  DQEELNKTKPIWTRNPDDITQEEYGEFYKSLTNDWEDHLAVKHFSVEGQLEFRALLFIPRRAPFDLFENK
          DQEELNKTKPIWTRN.D.ITQE.YGEF..S.TNDWEDHLAVKHFS.EGQLEFRALLFI...APFD.F.N.
Retrocopy DQEELNKTKPIWTRNHDYITQEKYGEFRNSHTNDWEDHLAVKHFSIEGQLEFRALLFIASQAPFDFFGNN

Parental  KKKNNIKLYVRRVFIMDSCDELIPEYLNFIRGVVDSEDLPLNISREMLQQSKILKVIRKNIVKKCLELFS
          KKK..IKLY...VFI..SCDELIPE.LNFIRG.VDSEDLPLNI..EMLQQSKILK.I..NIVK..LELF.
Retrocopy KKKDTIKLYILHVFIVHSCDELIPEDLNFIRGMVDSEDLPLNI-*EMLQQSKILKAIHENIVK*YLELFA

Parental  ELAEDKENYKKFYEAFSKNLKLGIHEDSTNRRRLSELLRYHTSQSGDEMTSLSEYVSRMKETQKSIYYIT
          ELAEDKENYKK.YE.FS.NLK.GI..D..N...LSELL..HTSQSG.EMTSLSEYV..........Y.IT
Retrocopy ELAEDKENYKKSYEVFSENLKFGIPQDAPNWQHLSELLHFHTSQSGEEMTSLSEYVXXXXXEGYTYY-IT

Parental  GESKEQVANSAFVERVRKRGFEVVYMTEPIDEYCVQQLKEFDGKSLVSVTKEGLELPEDEEEKKKMEESK
          GES.EQVA.SAFVE.V.KRGF.VVY.T.P.D.YC.QQLKEF.GK.L.SVTKEGLELPE.EEEKKKMEE.K
Retrocopy GESNEQVASSAFVE*VQKRGFKVVYNTNPTDKYCMQQLKEFNGKGLISVTKEGLELPEGEEEKKKMEECK

Parental  AKFENLCKLMKEILDKKVEKVTISNRLVSS-PCCIVTSTYGWTANMERIMKAQALRDNSTM-GYMMAKKH
          .K.ENLCK.MK.ILDKKV.KVT.SNRL.SS..CC.VTS.YG.TA.ME.I.KAQ.L.D.S.M.GY.MAK.H
Retrocopy VKLENLCKFMKIILDKKVDKVTVSNRLESS<TCCNVTSIYGLTAIMEQIVKAQVLWDTSMM<GYLMAKGH

Parental  LEI-NPDHPIVETLRQKAEADKNDKAVKDLVVLLFETALL
          L.I...DH.IVETL.QKAE.D.NDKAVKD.VVLL.ET.LL
Retrocopy LVI<HHDHCIVETLWQKAEVDNNDKAVKDWVVLLLETKLL

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	1230.31 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	1089.76 RPM
SRP007412_cerebellum	0.00 RPM	787.49 RPM
SRP007412_heart	0.00 RPM	930.98 RPM
SRP007412_kidney	0.00 RPM	474.76 RPM
SRP007412_liver	0.00 RPM	314.65 RPM
SRP007412_testis	0.04 RPM	376.63 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1319 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1319 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1319 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_880
Gorilla gorilla	retro_ggor_1011

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001981	4 retrocopies	retro_cfam_1108, retro_cfam_411, retro_cfam_562, retro_cfam_881,
Felis catus	ENSFCAG00000009764	1 retrocopy	retro_fcat_1177,
Homo sapiens	ENSG00000096384	2 retrocopies	retro_hsap_2912, retro_hsap_2958,
Macropus eugenii	ENSMEUG00000013735	1 retrocopy	retro_meug_1896,
Myotis lucifugus	ENSMLUG00000005239	2 retrocopies	retro_mluc_1604, retro_mluc_865,
Macaca mulatta	ENSMMUG00000011073	2 retrocopies	retro_mmul_1526, retro_mmul_2313,
Macaca mulatta	ENSMMUG00000022686	2 retrocopies	retro_mmul_1319 , retro_mmul_1869,
Macaca mulatta	ENSMMUG00000023469	1 retrocopy	retro_mmul_391,
Mus musculus	ENSMUSG00000023944	3 retrocopies	retro_mmus_1916, retro_mmus_3528, retro_mmus_856,
Rattus norvegicus	ENSRNOG00000019834	6 retrocopies	retro_rnor_1561, retro_rnor_1562, retro_rnor_1787, retro_rnor_597, retro_rnor_598, retro_rnor_87,
Tursiops truncatus	ENSTTRG00000006924	1 retrocopy	retro_ttru_292,