RetrogeneDB ID: retro_mmul_1301

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 17:70697130..70697986(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAR1
• Ensembl ID: ENSMMUG00000011990
• Aliases: None
• Description: None

Sequence

>retro_mmul_1301
GTTTCATTTGCACAACAAATAAAGAATCTGGAAGTGTTCATGCATGTATCAACAGCATATGCCTACTGTAATCAAAAGCA
TATTGATGAAGTAGTCTATCCACCACCTGTGGATCTCAAGAAGCTGATTGACTCTTTAGAGTGGATGGATTGTGGCCTAG
TAAATGATATCATGACAAAGTTGATAGGAGACAGACCTAACACATACATATACACAAAAGCATTGGCAGAATATGTTGTA
CAACAAGAAGGAACAAAGCTAAACGTGGAGATTGTAAGGCCATCTATTGTTGGTGCCAGTTGGAAAGAACATTTTCCAGG
ATGGATTGATAATTTTAATGGACCAAGTGGTCTCTTTATTGTGGCAGGGAAAGGAATTATTTGAACAATGCATGTCTCCA
ATAATGCCCTTGCAGATCTTGTTCCTTAGATGCAGTTGTGAACAAGAGTCTTGTGGCAGCCTGGTATTCCGGACTTAATA
GATCAAGAAACCTCATGGCATATAATTGTACAACAGATAGCACTAATCCTTTCCACTGGGTGAAGCTGAATACCATGTAA
TTTCCACTTTCAAGAGGAATCCTCTGGAGCAGACCTCCAAACGGCCCAATGTACATCTAACTTCCAGTCACCTTTTATAT
CATTACTGGATTGCTGTAAGTCATAAGGCCCCAGCATTCCTCTATGATATCTACCTCACGATGACTGGAAGAAGCCCAAG
GATGATGAAAACAATAACTCATCTTCACAAAGCTATGATGTTACTTGAGTATTTCACAAGTAATTCTTGGATTTGGAATA
CTGAAAATGTCAACATGTTAATGAATCAACTAAACCCTGAAGATAAAAGACTTTCA

Alignment

ORF - retro_mmul_1301 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.07 %
• Parental protein coverage: 55.21 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ILLAQQMKNLEVFMHVSTAYAYCNRKHIDEVVYPPPVDPKKLIDSLEWMDDGLVNDITPKLIGDRPNTYI
          ...AQQ.KNLEVFMHVSTAYAYCN.KHIDEVVYPPPVD.KKLIDSLEWMD.GLVNDI..KLIGDRPNTYI
Retrocopy VSFAQQIKNLEVFMHVSTAYAYCNQKHIDEVVYPPPVDLKKLIDSLEWMDCGLVNDIMTKLIGDRPNTYI

Parental  YTKALAEYVVQQEGAKLNVAIVRPSIVGASWKEPFPGWIDNFNGPSGLFIAAGKGILRTIRASNNALADL
          YTKALAEYVVQQEG.KLNV.IVRPSIVGASWKE.FPGWIDNFNGPSGLFI.AGKGI..T...SNNALADL
Retrocopy YTKALAEYVVQQEGTKLNVEIVRPSIVGASWKEHFPGWIDNFNGPSGLFIVAGKGII*TMHVSNNALADL

Parental  VP-VDVVVNMSLAAAWYSGVNRPRNIMVYNCTTGSTNPFHW-GEVEYHVISTFKRNPLEQAFRRPNVNLT
          VP..D.VVN.SL.AAWYSG.NR.RN.M.YNCTT.STNPFHW.GE.EYHVISTFKRNPLEQ...RPNV.LT
Retrocopy VP<LDAVVNKSLVAAWYSGLNRSRNLMAYNCTTDSTNPFHW<GEAEYHVISTFKRNPLEQTSKRPNVHLT

Parental  SNHLLYHYWIAVSHKAPAFLYDIYLRMTGRSPRMMKTITRLHKAMVFLEYFTSNSWVWNTDNVNMLMNQL
          S.HLLYHYWIAVSHKAPAFLYDIYL.MTGRSPRMMKTIT.LHKAM..LEYFTSNSW.WNT.NVNMLMNQL
Retrocopy SSHLLYHYWIAVSHKAPAFLYDIYLTMTGRSPRMMKTITHLHKAMMLLEYFTSNSWIWNTENVNMLMNQL

Parental  NPEDKKAS
          NPEDK..S
Retrocopy NPEDKRLS

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	62.97 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	30.86 RPM
SRP007412_cerebellum	0.00 RPM	74.58 RPM
SRP007412_heart	0.00 RPM	28.38 RPM
SRP007412_kidney	0.00 RPM	28.76 RPM
SRP007412_liver	0.00 RPM	3.17 RPM
SRP007412_testis	0.64 RPM	37.05 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1301 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1301 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1301 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1225
Pan troglodytes	retro_ptro_840
Gorilla gorilla	retro_ggor_958
Pongo abelii	retro_pabe_1019

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003490	2 retrocopies	retro_chof_1358, retro_chof_1733,
Callithrix jacchus	ENSCJAG00000010077	1 retrocopy	retro_cjac_545,
Cavia porcellus	ENSCPOG00000002654	1 retrocopy	retro_cpor_267,
Homo sapiens	ENSG00000197601	1 retrocopy	retro_hsap_1225,
Gorilla gorilla	ENSGGOG00000001180	1 retrocopy	retro_ggor_958,
Macaca mulatta	ENSMMUG00000011990	1 retrocopy	retro_mmul_1301 ,
Nomascus leucogenys	ENSNLEG00000017695	1 retrocopy	retro_nleu_698,
Oryctolagus cuniculus	ENSOCUG00000004336	2 retrocopies	retro_ocun_1056, retro_ocun_790,
Otolemur garnettii	ENSOGAG00000005064	2 retrocopies	retro_ogar_1353, retro_ogar_341,
Pongo abelii	ENSPPYG00000003470	1 retrocopy	retro_pabe_1019,
Pan troglodytes	ENSPTRG00000024190	1 retrocopy	retro_ptro_840,
Rattus norvegicus	ENSRNOG00000013176	1 retrocopy	retro_rnor_467,