RetrogeneDB ID: retro_mmul_1504

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 2:34244258..34245576(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.18411
• Ensembl ID: ENSMMUG00000011862
• Aliases: None
• Description: protein FAM214B [Source:RefSeq peptide;Acc:NP_001180805]

Sequence

>retro_mmul_1504
ATGTGCTACATGTAGGCAGAGCTGTCTCCACCCTCACAGCCAGAGGCTGGCCCTTCGCAGCCTCCAGTCAGGCAGGGAGC
CCTCCGGGGTGGCCTGTTCATGGGCTACAGCCCAGTAAGTGGAGGACGGGGAGCAGCAACATCCCCCAGGGTCTACCAGG
TATCCCTCCAGCTGGTGCCTCTGAGCCTCATAGGGCCCAGAAGCGACCAGCCTCTCCCACTGAGGGTCCCCAGGTACTGG
AGAGAGGCCCTGGGCTGGGGGCCAGAGAGGGATTACCCCTTGAAGAACCATCTCCTGTGGGGCTCTTGGGCCCAGGGGCA
CTGGGGCTGGGAGCAGGTGTGGCCAGCCACCATTTCTCCCACTGTGACCTCTGTGTTGTGGAACAGGGAAGTAGTGCTAC
CTGTTATTGGACTTCAGGGGACTGGAGTCCCCCCTGGCCCCAATCCTATGCTTCCTGAAATGCTTTGCACACCAGAGACA
GCCTCCCCAGATCCAGGGGGACAGGGGTCCCCGGGGGAGTCCCCAGGGCCAGCCCTCTGGGCCAGCTGCACACGCTCGAC
ACTGATTTGCAGTCTTGCACAAATAAGGGGTAAGAGCCCAGTGGCTGGGGTGGGCAATGGGGGGAGCCTCTGGCCTAGGG
AGTCCCTGGCATTGACAGTGGGCACAGTCCCAAACACACACCCCCAGTCTTGGACCTCCAGGCCCCTGCCCCACCAAGCA
AAGGCTGCTTCCTGCTGGAGAAGCCCCAAATGTCAGTTTCAAGGAAGAGGGGCCAGCCCTTTGGAGGTGCCAGGGAACCC
TGGGCCACCCCACTGCTGCCAACAGTTCTGATGCCCAAACCATACTCTTCTGGAGCCACCTGCTGCCTGGGCCCAACGAG
CCTGTTTTGGACCCAACAGACTGCAGTCCCATGGGGCGGAGGCTGAGAGGTGCCCATCATCCGAAGCTGAGCCCACTTTG
AAGCCGCTGGAAGGGGCCAGGCCTGCTGAGCCCCCCTCGTGCCTCCCCTCTTCCCACCCCTGTTGTCAGCTGTACCCTGC
TGGTCAACTTTGAGGAATCACTGCTGCAAGGACGCTTTGCACCATCTGGCCACATTGAGGGCTTCAAAGCAGAGACTGGA
GCTAGTGGGTCCTACTGCCACCACCATGTCACACTGCCTGTCACTGTCACGTTCTTTGAGGTTTCTGAGCAAAATGTCCC
CACCCCTTTCCTGGGCTTCATGGATCTGAACTCCCCAGGGAGGAAGAGTTACAGCGTGCCCAAAGTGGGCACTATGCAAG
TAACATTTAACCCCAACCAGACTATGGTGAAGATGTTC

Alignment

ORF - retro_mmul_1504 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.89 %
• Parental protein coverage: 82.16 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MRHVQAEPSPSSEPEAGPSQPPVRQGALQGGLLM-GYSPAGGAT-SPGVYQVSIFSPPAGTSEPHRALKR
          M....AE.SP.S.PEAGPSQPPVRQGAL.GGL.M.G..P....T.S....Q.....PPAG.SEPHRA.KR
Retrocopy MCYM*AELSPPSQPEAGPSQPPVRQGALRGGLFM<GLQPSKWRTGSSNIPQGLPGIPPAGASEPHRAQKR

Parental  QAPPTEGPRELKRGPGLGAREGLPPEEPSTVGLLGPEGLGLGLGVASQHFSHRGLCVVEQRSSVTSSWTS
          .A.PTEGP..L.RGPGLGAREGLP.EEPS.VGLLGP..LGLG.GVAS.HFSH..LCVVEQ.SS.T..WTS
Retrocopy PASPTEGPQVLERGPGLGAREGLPLEEPSPVGLLGPGALGLGAGVASHHFSHCDLCVVEQGSSATCYWTS

Parental  GTWS-PPCPPSNASCNTLHTRDWASPDPGGHGSLGESPGPAPPGQLH---TLDTDLHSLAQIGGKSPVAG
          G.WS.PP..P.......L.T...ASPDPGG.G....SPG..P...L....T..T...SLAQI.GKSPVAG
Retrocopy GDWS>PP-GPNPMLPEMLCTPETASPDPGGQG----SPGESPGPALWASCTRSTLICSLAQIRGKSPVAG

Parental  VGNGGSLLPRES-PGTANGHSPEHTPP-GPGPPGPCPTKRRLLPAGEAPDVSSEEEGPAPRRRRGSLGHP
          VGNGGSL.PRES.PG...GHSP.HTPP...GPPGPCPTK.RLLPAGEAP.VS..EEGPA..R..G.LGHP
Retrocopy VGNGGSLWPRES<PGIDSGHSPKHTPP<SLGPPGPCPTKQRLLPAGEAPNVSFKEEGPALWRCQGTLGHP

Parental  TAANSSDAKATSFWSHLLPGPKEPVLDPTDCSPMGRRLKGARRLKLSPLRSLRKGPGLLSPPSASPVPTP
          TAANSSDA....FWSHLLPGP.EPVLDPTDCSPMGRRL.GA...KLSPL.S..KGPGLLSPP.ASP.PTP
Retrocopy TAANSSDAQTILFWSHLLPGPNEPVLDPTDCSPMGRRLRGAHHPKLSPL*SRWKGPGLLSPPRASPLPTP

Parental  AVSRTLLGNFEESLLRGRFAPSGHIEGFTAEIGASGSYCPQHVTLPVTVTFFDVSEQNAPAPFLGIVDLN
          .VS.TLL.NFEESLL.GRFAPSGHIEGF.AE.GASGSYC..HVTLPVTVTFF.VSEQN.P.PFLG..DLN
Retrocopy VVSCTLLVNFEESLLQGRFAPSGHIEGFKAETGASGSYCHHHVTLPVTVTFFEVSEQNVPTPFLGFMDLN

Parental  PLGRKGYSVPKVGTVQVTLFNPNQTVVKMF
          ..GRK.YSVPKVGT.QVT.FNPNQT.VKMF
Retrocopy SPGRKSYSVPKVGTMQVT-FNPNQTMVKMF

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	18.04 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	30.94 RPM
SRP007412_cerebellum	0.00 RPM	12.72 RPM
SRP007412_heart	0.00 RPM	15.60 RPM
SRP007412_kidney	0.00 RPM	15.14 RPM
SRP007412_liver	0.04 RPM	11.76 RPM
SRP007412_testis	0.00 RPM	23.67 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1504 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1504 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1504 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2831
Pan troglodytes	retro_ptro_1919
Gorilla gorilla	retro_ggor_1966
Pongo abelii	retro_pabe_2200

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009210	1 retrocopy	retro_cjac_1357,
Homo sapiens	ENSG00000005238	1 retrocopy	retro_hsap_2831,
Gorilla gorilla	ENSGGOG00000003218	1 retrocopy	retro_ggor_1966,
Microcebus murinus	ENSMICG00000005528	1 retrocopy	retro_mmur_1580,
Macaca mulatta	ENSMMUG00000011862	1 retrocopy	retro_mmul_1504 ,
Nomascus leucogenys	ENSNLEG00000004530	1 retrocopy	retro_nleu_1207,
Pongo abelii	ENSPPYG00000019101	1 retrocopy	retro_pabe_2200,
Pan troglodytes	ENSPTRG00000020904	1 retrocopy	retro_ptro_1919,