RetrogeneDB ID: retro_mmul_716

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1099214740908:35050..35992(+)
• Located in intron of: ENSMMUG00000012091

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.4146
• Ensembl ID: ENSMMUG00000012044
• Aliases: None
• Description: None

Sequence

>retro_mmul_716
TCTGGGGATGCCGACATAGACCCAAAACTCCTGGAGCTCACCGCTGACGAGGAGAAGTGCCGCAGCATCCGCAGGCAGTA
CCGGCAGCTCATGTACTGCGTGCGGCAGAACCGGGAGGACATCGTGAACTCGGCGAACAACTCCTTGACCGAGGCTTTGG
AGGAAGCCAACGTCCTGTTTGATGGAGTGAGCCGAACCAGAGAAGCAGCCCTCGACGCCCAGTTTCTTGTCATGGCTTCT
GACTTGGGTAAAGAAAAGGCAAAGCAGTTAAACTCTGACCTGAACTTCTTTAATCAGTTAGCATTTTGTGACTTTCTGTT
TCTGTTCGGGGGTCTGAATTGGATGGAAGGCGAGCCTGACGACTTGAGTGATTGTGATGATAACATAGCTCTTTCCTTCT
GGAAGGCAATGGAAAAGGAAGCAACATCCTGGATGGTAAAAGCTGAGACATTCCATTTTGTTTTTGGTTCATTCAAACTA
GAACCTTCTGCACCAAAGCCCCGACTTGAACACCAGAAAAAAGTTCGCAAGATGGAGGAAAATGGGAATATGCCTACAAA
GTTGCGGAAGCTGGACCTGAGTAGTTATCCAGAAGCGACAGAAAAAAACGTAGAAAGGATTTTGGGATTGTTGCAAACCT
ACTTTCGAAAGTATCCTGATACTCCTGTGTCCTATTTTGAGTTTGTGATTGATCCAAACTCTTTTTCTCGTACTGTGGAG
AATATATTTTATGTTTCTTTTATTGTAAGAGATGGTTTTGCAAGAATAAGGCTTGATGAAGACAGGCTGCCAATATTAGA
GCCGATGAATGTTAACCAAATGGGTGAGGGAAATGATTCCAGTTGCCATGGTAGGAAACAGGGAGTCATATCTTTGACTT
TACAGGAGTGGAAAAACATTGTGGCAGCTTTTGAAATTTCTGAGGCTATGATTACATACTCC

Alignment

ORF - retro_mmul_716 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.57 %
• Parental protein coverage: 81.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SGDEMMDPASLEAEADQGLCRQIRHQYRALINSVQQNREDILN-AGDKLTEVLEEANTLFNEVSRAREAV
          SGD...DP..LE..AD...CR.IR.QYR.L...V.QNREDI.N.A...LTE.LEEAN.LF..VSR.REA.
Retrocopy SGDADIDPKLLELTADEEKCRSIRRQYRQLMYCVRQNREDIVNSANNSLTEALEEANVLFDGVSRTREAA

Parental  LDAHFLVLASDLGKEKAKQLRSDLSSFDMLRYVETLLTHMGVNPLEAEELIRDEDSPDFEFIVYDSWKIS
          LDA.FLV.ASDLGKEKAKQL.SDL..F..L.....L....G.N..E.E....D..S.....I....WK..
Retrocopy LDAQFLVMASDLGKEKAKQLNSDLNFFNQLAFCDFLFLFGGLNWMEGEP---DDLSDCDDNIALSFWKAM

Parental  GKTAENTFNKTHTFHFLLGSIYGECPVPKPRVDRPRKVPMIQEERAMPAQLRRME-ESHQEATEKEVERI
          .K.A.....K..TFHF..GS...E...PKPR.....KV....E...MP..LR.....S..EATEK.VERI
Retrocopy EKEATSWMVKAETFHFVFGSFKLEPSAPKPRLEHQKKVRKMEENGNMPTKLRKLDLSSYPEATEKNVERI

Parental  LGLLQTYFQEDPDTPMSFFDFVVDPHSFPRTVENIFHVSFIIRDGFARIRLDQDRLPIIEPVSINEENEG
          LGLLQTYF...PDTP.S.F.FV.DP.SF.RTVENIF.VSFI.RDGFARIRLD.DRLPI.EP...N...EG
Retrocopy LGLLQTYFRKYPDTPVSYFEFVIDPNSFSRTVENIFYVSFIVRDGFARIRLDEDRLPILEPMNVNQMGEG

Parental  FEHNTQVRNQGIIALSYRDWEEIVKTFEISEPVITPS
          .......R.QG.I.L....W..IV..FEISE..IT.S
Retrocopy NDSSCHGRKQGVISLTLQEWKNIVAAFEISEAMITYS

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	0.67 RPM	6.39 RPM
SRP007412_brain_prefrontal_cortex	0.40 RPM	4.92 RPM
SRP007412_cerebellum	0.45 RPM	15.95 RPM
SRP007412_heart	0.47 RPM	5.12 RPM
SRP007412_kidney	0.59 RPM	6.57 RPM
SRP007412_liver	0.20 RPM	1.98 RPM
SRP007412_testis	51.94 RPM	1.43 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_716 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_716 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_716 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_43
Bos taurus	retro_btau_1387
Canis familiaris	retro_cfam_379
Equus caballus	retro_ecab_109

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010897	1 retrocopy	retro_amel_419,
Bos taurus	ENSBTAG00000019166	1 retrocopy	retro_btau_1387,
Canis familiaris	ENSCAFG00000012419	2 retrocopies	retro_cfam_1427, retro_cfam_379,
Choloepus hoffmanni	ENSCHOG00000003695	1 retrocopy	retro_chof_577,
Dipodomys ordii	ENSDORG00000003880	1 retrocopy	retro_dord_677,
Equus caballus	ENSECAG00000016651	2 retrocopies	retro_ecab_109, retro_ecab_465,
Erinaceus europaeus	ENSEEUG00000014906	1 retrocopy	retro_eeur_124,
Felis catus	ENSFCAG00000003647	1 retrocopy	retro_fcat_994,
Homo sapiens	ENSG00000107672	1 retrocopy	retro_hsap_43,
Loxodonta africana	ENSLAFG00000004214	1 retrocopy	retro_lafr_1051,
Macaca mulatta	ENSMMUG00000012044	1 retrocopy	retro_mmul_716 ,
Mustela putorius furo	ENSMPUG00000002960	1 retrocopy	retro_mputfur_396,
Nomascus leucogenys	ENSNLEG00000016919	1 retrocopy	retro_nleu_2073,
Otolemur garnettii	ENSOGAG00000010026	1 retrocopy	retro_ogar_280,
Pongo abelii	ENSPPYG00000002712	1 retrocopy	retro_pabe_878,
Pteropus vampyrus	ENSPVAG00000017186	2 retrocopies	retro_pvam_1163, retro_pvam_795,
Rattus norvegicus	ENSRNOG00000020452	1 retrocopy	retro_rnor_2515,
Ictidomys tridecemlineatus	ENSSTOG00000011112	1 retrocopy	retro_itri_36,
Vicugna pacos	ENSVPAG00000006534	1 retrocopy	retro_vpac_260,