RetrogeneDB ID: retro_mmul_1814

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 4:4974677..4975613(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TFB2M
• Ensembl ID: ENSMMUG00000022915
• Aliases: None
• Description: None

Sequence

>retro_mmul_1814
ATGTCGCCAATCGTATAGAGAAAACAAAACAGACCTCCACACCTATTGCTGCAGTGCAATCCGGGTCCTGGAATCCTGAC
TCAGGCATTACTTGAAGTTGATGCCAAAGCGGTTGCCCTTGAAAGTGACAAAACTTTTATTGCACATTTGGAGTCCTTAG
GAAAAAATCTGGATGGAAAACTACAAGTGAGTCACTGTGACTTCTTTAAAATAGATCCTAGAAGTGGTGGAGTAATAAAA
CCACCTGCTATGGCTTCTCAAGGGCTGTTTCAGAATTTGGGAATAGAAGCAGTTCCTTGGACAGCAGGCATCCCTTGAAA
AGTAACTGGAATGTTCCCAAGTAGAGGTGAAGAAAGGGCATTTTGGAAACCTGCATATGACTTGTATTCCTGTACTTCTA
TATATAAATTTGGACGAATAGAATGAAATATCTTTATTGGTGAAAAAGAATTCCAGAAACTAACAGCAGATACCCGAAAT
CCAGACTTGTATCATGTATGAAGTGTTATCTGGCACGCAGCTTGTGAGATTAAGGTTCTGCACATGGAGCCTTGGTCATC
ATTTGATGTGTACACCCGAAATGGGCGGCTGGAAAACCCAAAGCATAGGGAATTATTAGAACTATTACAACACAATCTGT
ATCTTATTCGAATGACTCCTTGTGGAAATTTATTTACCAAGAACTTAACACTTATTCACTATAATATATTTTTTCACATG
TTAAAGCACTGTTTTGTGAGGCGCAGTGCCAATGTAATAGACCACTTACGTTCACTGACTCCACTTGATGCAATGGATAT
ATTGCCGCAAATAGGAAAAAAGGAAGAAGAGAAAATAACTAACGTGTACCCTCAAAACTTCAAAAAACTTTTTGAAACTA
TAGAGTGTTCCAAAGATTGTGCTTATAAATGGCTATATGATGAAACCCTGGAAGAT

Alignment

ORF - retro_mmul_1814 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.95 %
• Parental protein coverage: 79. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LAQIVCGKPNRPPHLLLECNPVNAPGPGILTEALLEAGATVVALESDKTFIPHLESLGKNLDGKLRVIHC
          ...IV..K.NRPPHLLL.CN....PGPGILT.ALLE..A..VALESDKTFI.HLESLGKNLDGKL.V.HC
Retrocopy MSPIV*RKQNRPPHLLLQCN----PGPGILTQALLEVDAKAVALESDKTFIAHLESLGKNLDGKLQVSHC

Parental  DFFRIDPRSGGAIKPPAMSSEGLFKNLGVEEVPWTAGVPLKVFGMFPSRGEKRALWKLAYDLYSCSSIYK
          DFF.IDPRSGG.IKPPAM.S.GLF.NLG.E.VPWTAG.P.KV.GMFPSRGE.RA.WK.AYDLYSC.SIYK
Retrocopy DFFKIDPRSGGVIKPPAMASQGLFQNLGIEAVPWTAGIP*KVTGMFPSRGEERAFWKPAYDLYSCTSIYK

Parental  FGRIEINMFIGEKEFQKLMADPRNRGLYYVLSVVWQVACEIKVLHMEPWSSFDVYTRSGRLENTKRKEVL
          FGRIE.N.FIGEKEFQKL.AD.RN..LY.V.SV.W..ACEIKVLHMEPWSSFDVYTR.GRLEN.K..E.L
Retrocopy FGRIE*NIFIGEKEFQKLTADTRNPDLYHV*SVIWHAACEIKVLHMEPWSSFDVYTRNGRLENPKHRELL

Parental  ELLQQNLYLIQMTPRRNLFANSLTPMNYNIFFHLLKHCFGKRSATVIDHLRSLTPLDAADILMQIGKKED
          ELLQ.NLYLI.MTP..NLF...LT...YNIFFH.LKHCF..RSA.VIDHLRSLTPLDA.DIL.QIGKKE.
Retrocopy ELLQHNLYLIRMTPCGNLFTKNLTLIHYNIFFHMLKHCFVRRSANVIDHLRSLTPLDAMDILPQIGKKEE

Parental  EKVVNMYPEDFKRLFETIESSEDCTYKWLYDDTLED
          EK..N.YP..FK.LFETIE.S.DC.YKWLYD.TLED
Retrocopy EKITNVYPQNFKKLFETIECSKDCAYKWLYDETLED

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	9.41 RPM
SRP007412_brain_prefrontal_cortex	0.16 RPM	8.49 RPM
SRP007412_cerebellum	0.77 RPM	9.56 RPM
SRP007412_heart	0.00 RPM	9.42 RPM
SRP007412_kidney	0.12 RPM	23.12 RPM
SRP007412_liver	0.20 RPM	11.80 RPM
SRP007412_testis	0.04 RPM	4.82 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1814 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1814 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1814 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3548
Pan troglodytes	retro_ptro_2412

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000013225	1 retrocopy	retro_cpor_451,
Homo sapiens	ENSG00000162851	1 retrocopy	retro_hsap_3548,
Gorilla gorilla	ENSGGOG00000001095	1 retrocopy	retro_ggor_2396,
Myotis lucifugus	ENSMLUG00000003923	1 retrocopy	retro_mluc_1302,
Macaca mulatta	ENSMMUG00000022915	1 retrocopy	retro_mmul_1814 ,
Nomascus leucogenys	ENSNLEG00000004146	1 retrocopy	retro_nleu_2323,
Oryctolagus cuniculus	ENSOCUG00000013727	2 retrocopies	retro_ocun_1557, retro_ocun_236,
Otolemur garnettii	ENSOGAG00000007823	2 retrocopies	retro_ogar_1444, retro_ogar_2187,
Pongo abelii	ENSPPYG00000000046	1 retrocopy	retro_pabe_3039,
Pan troglodytes	ENSPTRG00000002188	1 retrocopy	retro_ptro_2412,