RetrogeneDB ID: retro_mmul_1121

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 14:108412057..108412781(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TFAM
• Ensembl ID: ENSMMUG00000019829
• Aliases: None
• Description: None

Sequence

>retro_mmul_1121
CTTCAAAGTGTGTGGGGCATGCTGAGTGCCCAGTGAAGGTCCAGAGTGGAGCTGTGCACTGGCTGTGGAAGTTGATTGTG
CTTACCTTTCAGTTTTGTGTATTTATTGAAATGGTTTTCATCCATCTTAGCTAGTTATCTGAAGAAACCTATGGTGTCTT
ACCTTCGGTTTTTGAAAGAATAGCTACTCATATTTAAAGCTCAGAACCCAGATGCAAAAAATTCAGAATTAATTAAAAGA
ATCACTGAGCTATGGAGAAAACTTGCTGAATCAGAGACAAAAAATATGAAGATGCTTACAGGGCAGACTGGCGGGCATTC
AGAGAAGAGAAAAAACAGAATTCAAGAACAGCTAACTCCAAGTCAGATAATATCTTTGGAAAAGAAATCATGCAAAAACT
TTAATAAAAGAAAGCGTTAATAAAAAAGAGAGAGCTTAACGATGCTTGGAAAACCAAAAGACTTTGCTCAGCTTACAACA
TTTTTGTATCTGAAAGCTTCCAAGAAGCTAAGGATGGTTCATCACAGGCAAAGCTGAAGACTGCAAATGAAAACTGGAAA
AATCTGTCAGGTTCTCAAAACAAGTGTACATTCAGCTTGCTAAAGATGATAAGATTCATTATGATAATGAAATTAAGCCT
TGGGAAGAACAAATGATTGAAGTTGGATGAAATGATTTTATACATCTTGAAATGAAGCAACCACCAAAATATGGCACTGA
GGAG

Alignment

ORF - retro_mmul_1121 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.5 %
• Parental protein coverage: 97.58 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LRSMWGVLNALGRSGAELCSGCGSRLRSPFSFVYLPKWFSSVLASCPKKPVSSYLRFSKQQLPIYRAQNP
          L.S.WG.L.A..RS..ELC.GCGS.L..PFSFVYL.KWFSS.LAS..KKP..SYLRF.K..L.I..AQNP
Retrocopy LQSVWGMLSAQ*RSRVELCTGCGS*LCLPFSFVYLLKWFSSILASYLKKPMVSYLRFLKE*LLIFKAQNP

Parental  DAKTTELVRRIAKHWRELPDSE-KKIYRDAYKAEWEVYKE-KISKFKEQLTPDEITSLE-KEILDKRLKR
          DAK..EL..RI...WR.L..SE..K.Y.DAY.A.W....E.......EQLTP..I.SLE.KEI..K....
Retrocopy DAKNSELIKRITELWRKLAESE<DKKYEDAYRADWRAFRE>RKNRIQEQLTPSQIISLE<KEIMQKL**K

Parental  KAVTKRKELIQLGKPKRPRSAYNVYVAERFQEAKGESPQEKLKTVKENWKNLSDSE-KELYIQHAKEDEI
          KA..K..EL....K.KR..SAYN..V.E.FQEAK..S.Q.KLKT..ENWKNLS.S..K..YIQ.AK.D.I
Retrocopy KALIKKRELNDAWKTKRLCSAYNIFVSESFQEAKDGSSQAKLKTANENWKNLSGSQ<KQVYIQLAKDDKI

Parental  RYHNEMKSWEEHMIEIGRKDVLRRTIKQRQKYGAEE
          .Y.NE.K.WEE.MIE.G..D......KQ..KYG.EE
Retrocopy HYDNEIKPWEEQMIEVG*NDFIHLEMKQPPKYGTEE

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	12.21 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	9.28 RPM
SRP007412_cerebellum	0.00 RPM	14.72 RPM
SRP007412_heart	0.00 RPM	9.54 RPM
SRP007412_kidney	0.00 RPM	16.43 RPM
SRP007412_liver	0.00 RPM	5.70 RPM
SRP007412_testis	0.00 RPM	117.45 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1121 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1121 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1121 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000000535	1 retrocopy	retro_dnov_536,
Dipodomys ordii	ENSDORG00000014013	2 retrocopies	retro_dord_415, retro_dord_691,
Erinaceus europaeus	ENSEEUG00000006119	3 retrocopies	retro_eeur_103, retro_eeur_182, retro_eeur_652,
Homo sapiens	ENSG00000108064	2 retrocopies	retro_hsap_3692, retro_hsap_923,
Gorilla gorilla	ENSGGOG00000004948	2 retrocopies	retro_ggor_2496, retro_ggor_745,
Loxodonta africana	ENSLAFG00000012891	1 retrocopy	retro_lafr_1164,
Macropus eugenii	ENSMEUG00000008802	1 retrocopy	retro_meug_190,
Macaca mulatta	ENSMMUG00000019829	1 retrocopy	retro_mmul_1121 ,
Nomascus leucogenys	ENSNLEG00000012295	2 retrocopies	retro_nleu_2827, retro_nleu_288,
Oryctolagus cuniculus	ENSOCUG00000014405	1 retrocopy	retro_ocun_1278,
Pongo abelii	ENSPPYG00000002430	2 retrocopies	retro_pabe_3042, retro_pabe_796,
Pan troglodytes	ENSPTRG00000002519	1 retrocopy	retro_ptro_641,
Rattus norvegicus	ENSRNOG00000000613	1 retrocopy	retro_rnor_1936,
Tursiops truncatus	ENSTTRG00000009246	1 retrocopy	retro_ttru_1763,