RetrogeneDB ID: retro_mmul_446

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:194184319..194184931(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NMNAT1
• Ensembl ID: ENSMMUG00000005863
• Aliases: None
• Description: nicotinamide nucleotide adenylyltransferase 1 [Source:HGNC Symbol;Acc:17877]

Sequence

>retro_mmul_446
TACCAGGAGAATGGACTCATTCCTGCCCATCACTGGGTCATCATGTCAAAACTTGCCACCAAGAATGCCAAATGGGTGGA
AGCTGATACATGGAAAAGTCTTCAGAAGGAGCGGATAGAGATGTTAAGGTGCTTATACAACATCAGGAGAAACTGGAGGT
TAGTAACGGTGATAACCAGCAGAATGTGCGTACACTAGAAAGGCCTGGACAAAAGAGGAAGTGCACTGAACAAAAACAGG
ATTCTAGTTGAAAGAAATCCCTGGAGTCCAAAACAAAAGGTATGACAAAAGTCAAGCTGTTGTGCGGGACAGATTATTGG
AGTCCTTTGGTGTTCCCAATTTGTGGAAGGGAGAAGACATCACCCAAATTGTGGCAGAATATGAGTTCACATGTATACTC
AGGCTGGAAATGATGCTCAGAAATTCATCCACGAATCTGGCATGCTGTGAAAACACTGGAGCAATATTCACATAGCGAAT
GAATGGATCACTAATGATATCTCATCTACAACAATCCGGAGAGCTCTCAGAAGGGGACAGAGCATTTGCTACTTGATATG
AGAACTTGTCCAAGAATAAATCAAAAAGCAAAATTTGTAATTATCAAAAAGT

Alignment

ORF - retro_mmul_446 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.67 %
• Parental protein coverage: 73.12 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  YKKKGLIPAYHRVIMAELATKNSKWVEVDTWESLQKEWKETL-KVLRHHQEKLEASNCGHPQNSPTLERL
          Y...GLIPA.H.VIM..LATKN.KWVE.DTW.SLQKE..E.L.KVL..HQEKLE.SN....QN..TLER.
Retrocopy YQENGLIPAHHWVIMSKLATKNAKWVEADTWKSLQKERIEML<KVLIQHQEKLEVSNGDNQQNVRTLERP

Parental  GRKRKWTE-KQDSSQKKSLEPKTKAVPKVKLLCGAD-LLESFAVPNLWKSEDITQIVANYGLICV-TRAG
          G.KRK.TE.KQDSS.KKSLE.KTK...KVKLLCG.D.LLESF.VPNLWK.EDITQIVA.Y...C..T.AG
Retrocopy GQKRKCTEQKQDSS*KKSLESKTKGMTKVKLLCGTD<LLESFGVPNLWKGEDITQIVAEYEFTCI<TQAG

Parental  NDAQKFIYESDVLWKHRSNIHVVNEWITNDISSTKIRRALRRGQSIRYLVPDLVQEYIEKHNLYSSES
          NDAQKFI.ES..L.KH.SNIH..NEWITNDISST.IRRALRRGQSI.YL...LVQE.I.K.NL..S.S
Retrocopy NDAQKFIHESGML*KHWSNIHIANEWITNDISSTTIRRALRRGQSICYLI*ELVQE*IKKQNL*LSKS

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	3.70 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	5.79 RPM
SRP007412_cerebellum	0.00 RPM	3.68 RPM
SRP007412_heart	0.00 RPM	6.30 RPM
SRP007412_kidney	0.00 RPM	10.80 RPM
SRP007412_liver	0.00 RPM	3.29 RPM
SRP007412_testis	0.00 RPM	4.37 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_446 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_446 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_446 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_247
Callithrix jacchus	retro_cjac_1690

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001361	2 retrocopies	retro_btau_1153, retro_btau_1654,
Callithrix jacchus	ENSCJAG00000005483	1 retrocopy	retro_cjac_1690,
Homo sapiens	ENSG00000173614	3 retrocopies	retro_hsap_247, retro_hsap_2740, retro_hsap_2989,
Macaca mulatta	ENSMMUG00000005863	2 retrocopies	retro_mmul_1488, retro_mmul_446 ,
Nomascus leucogenys	ENSNLEG00000009375	2 retrocopies	retro_nleu_1072, retro_nleu_741,
Oryctolagus cuniculus	ENSOCUG00000023212	1 retrocopy	retro_ocun_1243,
Otolemur garnettii	ENSOGAG00000033037	2 retrocopies	retro_ogar_1088, retro_ogar_637,