RetrogeneDB ID: retro_mmul_1146

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 15:44241360..44242131(+)
• Located in intron of: ENSMMUG00000007724

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.2381
• Ensembl ID: ENSMMUG00000016022
• Aliases: None
• Description: transcription elongation factor A protein 1 [Source:RefSeq peptide;Acc:NP_001247637]

Sequence

>retro_mmul_1146
GAAGACAAGGTCGTTCCCATTGCCAACTAAATGGACAAGATGGTGCAGAAGAATACAGCTGATGCATTGGATTTGCCAAA
GGAGCTTAAAAGTATTCCCATGACCTTGGAATTATTACAGCCCAGAGAAGAATCAGAATATCAGTTAATGCTAATGGCAA
GCAGCATAAAGAGGAAGAAGTTATATCTTCAACAGTCTGTCATGAAATCTGGGAAAAAGTTACTATCAACCAAGAAAGAC
CCTGAAGAAAAGAAAAAAGAACCTGTAGTAACATTGCAGAATAGCCCTGAAGCGAGAGAAGAAAGTAGCTCCGGTGGCAA
TGCAAGCAGCAGAAAGGGTGAGACAAATGCTCTAGATACTCGTGTTTCATCCTTTATTCAGGAATGAAGCACTTCTGACC
CTGCTTGGTTAAAGTGTTGGGAGGTGCTTGCTGCAGCTCTCGGAACAGGAGATGGCTACACTGCTATTGGAACTGGTGAG
GAAGAATTAGGATCTCAAATTGAGGAGACTGCATATCAAGAAATTAAGGAATATAGATACAAAATGCAAAGGTGGAGTAT
GAAGTAGGATATCAAATCTTAAAGAGCAAAGAATCCAAATTTAAGGGAAAATGTACCATGTGAGAATATTCCTAATGTCT
TATTTGCTAGAATGATGGCACAGGAAATGTCCAGTGATGGGCTCAGAGAGATATGGAAAAACTTGACCAAAGAAGCCATC
AGAGAGCATTAGGTGACCAAGGCAAGTGGAACCCAGAGTGGCTTGTTCACA

Alignment

ORF - retro_mmul_1146 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.5 %
• Parental protein coverage: 86.71 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EDEVVRFAKKMDKMVQKKNAAGALDLLKELKNIPMTLELLQSTRIGMSVNAIRKQSTDEEVTSLAKSLIK
          ED.VV..A..MDKMVQK.N.A.ALDL.KELK.IPMTLELLQ..............S.......L..S..K
Retrocopy EDKVVPIAN*MDKMVQK-NTADALDLPKELKSIPMTLELLQPREESEYQLMLMASSIKRKKLYLQQSVMK

Parental  SWKKLLDGPSTEKDLDEKKKEPAITSQNSPEAREESTSSGNVSNRKDETNARDTYVSSFPRAPSTSDSVR
          S.KKLL...ST.KD..EKKKEP..T.QNSPEAREES.S.GN.S.RK.ETNA.DT.VSSF....STSD...
Retrocopy SGKKLL---STKKDPEEKKKEPVVTLQNSPEAREESSSGGNASSRKGETNALDTRVSSFIQE*STSDPAW

Parental  LKCREMLAAALRTGDDYIAIGADEEELGSQIEEAIYQEI-RNTDMKYKNRVRSRISNLKD-AKNPNLRKN
          LKC.E.LAAAL.TGD.Y.AIG..EEELGSQIEE..YQEI.RN.D.K.K..V.SRISNLK..AKNPNLR.N
Retrocopy LKCWEVLAAALGTGDGYTAIGTGEEELGSQIEETAYQEI>RNIDTKCKGGV*SRISNLKE<AKNPNLREN

Parental  VLCGNIPPDLFARMTAEEMASDELKEMRKNLTKEAIREHQMAKTGGTQTDLFT
          V.C.NIP..LFARM.A.EM.SD.L.E..KNLTKEAIREH...K..GTQ..LFT
Retrocopy VPCENIPNVLFARMMAQEMSSDGLREIWKNLTKEAIREH*VTKASGTQSGLFT

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	0.22 RPM	26.56 RPM
SRP007412_brain_prefrontal_cortex	0.16 RPM	19.28 RPM
SRP007412_cerebellum	0.52 RPM	24.60 RPM
SRP007412_heart	0.00 RPM	15.43 RPM
SRP007412_kidney	0.23 RPM	19.95 RPM
SRP007412_liver	0.08 RPM	17.18 RPM
SRP007412_testis	0.30 RPM	26.31 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1146 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1146 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1146 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001247	1 retrocopy	retro_chof_458,
Callithrix jacchus	ENSCJAG00000014407	1 retrocopy	retro_cjac_2095,
Dasypus novemcinctus	ENSDNOG00000013799	4 retrocopies	retro_dnov_1315, retro_dnov_1853, retro_dnov_839, retro_dnov_952,
Erinaceus europaeus	ENSEEUG00000009220	1 retrocopy	retro_eeur_73,
Homo sapiens	ENSG00000187735	4 retrocopies	retro_hsap_2634, retro_hsap_4159, retro_hsap_4200, retro_hsap_4243,
Gorilla gorilla	ENSGGOG00000023652	3 retrocopies	retro_ggor_2794, retro_ggor_2814, retro_ggor_2844,
Macaca mulatta	ENSMMUG00000016022	1 retrocopy	retro_mmul_1146 ,
Mus musculus	ENSMUSG00000033813	2 retrocopies	retro_mmus_1369, retro_mmus_3559,
Nomascus leucogenys	ENSNLEG00000000981	3 retrocopies	retro_nleu_1028, retro_nleu_1374, retro_nleu_1384,
Oryctolagus cuniculus	ENSOCUG00000007474	3 retrocopies	retro_ocun_1382, retro_ocun_401, retro_ocun_852,
Pongo abelii	ENSPPYG00000018589	3 retrocopies	retro_pabe_3395, retro_pabe_3436, retro_pabe_3455,
Pan troglodytes	ENSPTRG00000020251	2 retrocopies	retro_ptro_2851, retro_ptro_2884,
Rattus norvegicus	ENSRNOG00000022323	1 retrocopy	retro_rnor_1089,
Sarcophilus harrisii	ENSSHAG00000013661	1 retrocopy	retro_shar_50,
Ictidomys tridecemlineatus	ENSSTOG00000021179	1 retrocopy	retro_itri_1745,
Tarsius syrichta	ENSTSYG00000001030	1 retrocopy	retro_tsyr_1624,