RetrogeneDB ID: retro_mmul_2395

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 9:44977312..44978896(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.2909
• Ensembl ID: ENSMMUG00000017696
• Aliases: None
• Description: None

Sequence

>retro_mmul_2395
GGATCAGAAGGACTCTGTATGGTGAATGCACCACCATGTTTTGCAGAAAGCATAGTGTTTCCAAGGAAATCTCAGGAAAA
TTACAAAGTCTATAACTTGAGCAACAGTTGGACCCTCATTTGTTGGGGCAAAGGAAAAAAATTATAAATATTATCTGTGT
CACTAACATGGGTTTACTACACTTCTTCTACCTCCAAATGCACTTTGCCTTGAATTCTTACCAAAAACCCGTGTCCTGGC
AATATAGCAGCCCTACACTTCCCTACACATGGCACTGCTGGGAGACTCAACCTGCAACTCCATCACGTGAGAGTGGGGTG
TGCTTGAAGTCTTTCATCAAGAAAAAAATGCAAATTGGTATCCATCTGGTCAGATGATGAAACTGTTTTGTGTCCAAAAT
GTTAACAATAAAGTTCACTTCCTTGTAAATGACAATTTTATAAAATTATAAGTAAATTGTCTTTGCAAAACATTAATTGT
GAGTTATCGCTTGGACTCCAGTCACACAGGGGTCTGTCCATGTTCCAGGAGTAAGGGTGTACTTTCATTTGTTGTATTAT
ACTCGTACCCCAACTTTTTTGGACCTCATGCAGCTTTAGCGAACAGCAGTTTCTCTAAGCTGATAAGGTTACAATGCTGT
GGAATGAAAAAGCCGCTGCTGGCTTGTAATAGCGAGAACAGATGTTGACAAGACAAGAACTTCCTGCTATGGGGAACAAA
GGCTGCATTGCACTGCAACCAATGGAGAAAATGCTGTCATTTGTTCAATTACCAAAACATAGCCCCATTTATGATATAAT
TTGGAATTCTGGTTCTACTGAGTTTTATGCTATATATGGTTTTATGCCTGCCAAAGCTATGATTTTCAACCTGAAATGTG
ATCTTGTGTTTGACCTTGGAACTGGTGCTCTAAGGCAGCCTATTTGGCCCTTGTGGCCATATATTAATACTAACTGGATT
CGGAAATCTGAAGAACAAACGTGAGTGTGGGATATTAAAAGCTACAAACTTATTTCCAAACAAGTAGCCTCTGTTCATAC
ATATTATGCTAGGTACCTAGATGGGAGCACCTTTTACTATCACACATGCTCCCAGGTTGTGTGTTAATAATGGATACAAG
CTTTGACATTATACCAGTCCTGTCCTGCATGAGTAAGATGTGTCATCAAATGTAGAAATATGGCAGGTTTCTTGGCAGCC
ATTTCTGGATGGACTATTTCCAGCAAAAGCAGTAACTTATCAAGCAGTTCCAAGTGAAGCACCCAACTAGGAACCTAACT
TTACAATGACTGATAGACTCCCAGCTTTAAGAAATAAACCAATCACCAATTCTAAGCTGCATAAAGAGAAATCACCCCAG
AATAAGAAATCACAACCAGGAAATGATAAACCATGATCAAAAGCAGCCCTGAAAAATCAAAGGAAATATAAAGCTAAGAA
AACTGCAAAGCAGGAAGTAAGAAGTGACAAGAGTCCAGATTTGACACCTACCTCTGTCCCGCAGAGCACACCCTGAAATA
CAGTGTCTCAGTTAACATCTGGAAACACTGAGATAGATGAAAATCCAAGAATCTAAAAAGCCAA

Alignment

ORF - retro_mmul_2395 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.38 %
• Parental protein coverage: 90.94 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 19

Retrocopy - Parental Gene Alignment:

Parental  GSEGLYMVNGPPHFTESTVFPRESGKNCKVYTFSKDGTLFAW-GNGEKV-NIISVINKGLLHSFDL-PKA
          GSEGL.MVN.PP.F.ES.VFPR.S..N.KVY..S...TL..W.G...K..NII.V.N.GLLH.F.L.P.A
Retrocopy GSEGLCMVNAPPCFAESIVFPRKSQENYKVYNLSNSWTLICW<GQRKKIINIICVTNMGLLHFFYL<PNA

Parental  VCLEFSPKNTVLATWQPYTT-SKDGTAGIPNLQLYDVK-TGTCLKSFIQKKTQ-NWCPS-WSEDETL-CA
          .CLEF.PK..VLA..QPYT.....GTAG..NLQL..V...G.CLKSFI.KK.Q.NW.PS.WS.DET..C.
Retrocopy LCLEFLPKTRVLAI*QPYTS<PTHGTAGRLNLQLHHVR<SGVCLKSFIKKKMQ<NWYPS<WSDDETV>CV

Parental  RNVNNEVHFFENNNF-NTIANKLHLQKINDFVLSPGPQPYKV-AVYVPG-SKGAPSFVRLYQYPNFAGPH
          .NVNN.VHF..N.NF...I..KL.LQ.IN...LS.G.Q......V.VPG.SKG..SFV.LY.YPNF.GPH
Retrocopy QNVNNKVHFLVNDNF<YKIISKLSLQNIN-CELSLGLQSHRG<SVHVPG<SKGVLSFVVLYSYPNFFGPH

Parental  AALANKSFFK-ADKVTMLWNKKATAVL-VIASTDVDKTGASYYGEQTLHYIATNGESAVV-QLPKNGP-I
          AALAN.SF.K.ADKVTMLWN.KA.A.L.VIA.TDVDKT..S.YGEQ.LH..ATNGE.AV.....K..P.I
Retrocopy AALANSSFSK<ADKVTMLWNEKAAAGL<VIARTDVDKTRTSCYGEQRLHCTATNGENAVICSITKT*P>I

Parental  YDVVWNSSSTEFCAVYGFMPAKATIFNLRCDPVFDFGTGP-RNAAY-YSPHGHILVLAGFGNLRGQME-V
          YD..WNS.STEF.A.YGFMPAKA.IFNL.CD.VFD.GTG....AAY...P.GHIL.L.GFGNL....E.V
Retrocopy YDIIWNSGSTEFYAIYGFMPAKAMIFNLKCDLVFDLGTGA<SKAAY<FGPCGHILILTGFGNLKNKRE<V

Parental  WDVKNYKLISKPVASDSTYFAWCPDG-EHIL-TATCAPRLRVNNGYKIWHYTGSILHKYDVPSNAELWQV
          WD.K.YKLISK.VAS..TY.A...DG.EH.L.T.T.APRL.VNNGYK..HYT...LH..DV.SN.E.WQV
Retrocopy WDIKSYKLISKQVASVHTYYARYLDG<EHLL<TITHAPRLCVNNGYKL*HYTSPVLHE*DVSSNVEIWQV

Parental  SWQPFLDGVFPAKTITYQAVPSEVPSEEPKVATAYRPPALRNKPITNSKLHEEEPPQNMKSQSGNDKPLS
          SWQPFLDG.FPAK..TYQAVPSE.P..EP......R.PALRNKPITNSKLH.E..PQN.KSQ.GNDKP.S
Retrocopy SWQPFLDGLFPAKAVTYQAVPSEAPN*EPNFTMTDRLPALRNKPITNSKLHKEKSPQNKKSQPGNDKP*S

Parental  KTALKNQRKHEAKKAAKQEARSDKSPDLAPTPAPQSTPRNTISQSISGDPEIDK-KIKNLKKK
          K.ALKNQRK..AKK.AKQE.RSDKSPDL.PT..PQSTP.NT.SQ..SG..EID..K.KNLK..
Retrocopy KAALKNQRKYKAKKTAKQEVRSDKSPDLTPTSVPQSTP*NTVSQLTSGNTEIDE<KSKNLKSQ

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	45.83 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	28.80 RPM
SRP007412_cerebellum	0.00 RPM	56.63 RPM
SRP007412_heart	0.00 RPM	30.91 RPM
SRP007412_kidney	0.00 RPM	43.54 RPM
SRP007412_liver	0.00 RPM	18.09 RPM
SRP007412_testis	0.26 RPM	15.49 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2395 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2395 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2395 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_565
Pan troglodytes	retro_ptro_423
Gorilla gorilla	retro_ggor_509
Pongo abelii	retro_pabe_517

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001199	1 retrocopy	retro_cjac_968,
Dasypus novemcinctus	ENSDNOG00000014002	1 retrocopy	retro_dnov_1148,
Homo sapiens	ENSG00000144895	1 retrocopy	retro_hsap_565,
Gorilla gorilla	ENSGGOG00000015391	1 retrocopy	retro_ggor_509,
Loxodonta africana	ENSLAFG00000003767	1 retrocopy	retro_lafr_502,
Macaca mulatta	ENSMMUG00000017696	1 retrocopy	retro_mmul_2395 ,
Nomascus leucogenys	ENSNLEG00000003219	1 retrocopy	retro_nleu_2213,
Oryctolagus cuniculus	ENSOCUG00000016095	3 retrocopies	retro_ocun_1771, retro_ocun_1825, retro_ocun_1861,
Pongo abelii	ENSPPYG00000029636	2 retrocopies	retro_pabe_517, retro_pabe_652,
Pan troglodytes	ENSPTRG00000015528	1 retrocopy	retro_ptro_423,
Ictidomys tridecemlineatus	ENSSTOG00000003374	1 retrocopy	retro_itri_1706,