RetrogeneDB ID: retro_mmul_2156

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 7:69925801..69926387(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PERP
• Ensembl ID: ENSMMUG00000000997
• Aliases: None
• Description: None

Sequence

>retro_mmul_2156
GTGATCCGCTGCAGCCTGGCCTGCGAGCGCTGCAGCTGGATCCTGACCCTGCTCCTACTCAGCGCCATCGCCTTTGACAT
CATAGCCCTGGCCGGCCGCGGCAGGCGGCAGTCAAGCGACCACGTCCAGACGTCCTTGCTATGGTGGAGATGTTTCCACG
AGGGCAGCGACGGCAGCGGGTCCTAAGAGGACGGCTGCTAGAGCCTCATGGAGTACGCGTTGGGTAGAGCAGCAGCTGCC
ATGCTCTTCTGGGGCTTCAGCATCCTGGTGATCTGTTTCATCCTCTCCTTCTTCTTCATCCTGTGTGTACCCCAGATGCT
TGTCTTCCTAAGAGTGATTGGAGGTCTCTTTGTCTTGGTTGCTGTGTTCCAGATCATCTCCCTGGTAATTTACCCCGTGA
AGTACACCCAAACCTTCAACCTTCAGGCCAGCCCTTGCTGTCACTTACATCTATAACTGGCCCTACGGCTTTGGGTGGGC
AGCCACGATTATCCTCATCAGCTGCGCTTTCTTCTGCTACTGCCTCCCCAACAATGAAGATGACCTCCTGGGCAATACCA
AGCCTAAGGACTTCTACACATCTGCC

Alignment

ORF - retro_mmul_2156 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.61 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MIRCGLACERCRWILPLLLLSAIAFDIIALAGRGWLQSSSHMQTSSLWWKCSQEGG-GSGSYEEGCQSLM
          .IRC.LACERC.WIL.LLLLSAIAFDIIALAGRG..QSS.H.QTS.LWW.C..EG..GSGS.E.GC.SLM
Retrocopy VIRCSLACERCSWILTLLLLSAIAFDIIALAGRGRRQSSDHVQTSLLWWRCFHEGSDGSGS*EDGC*SLM

Parental  EYAWGRAAAAMLFCGFIILVICFILSFF-ALCGPQMLVFLRVIGGLLALAAVFQIISLVIYPVKYTQTFA
          EYA.GRAAAAMLF.GF.ILVICFILSFF..LC.PQMLVFLRVIGGL..L.AVFQIISLVIYPVKYTQTF.
Retrocopy EYALGRAAAAMLFWGFSILVICFILSFFFILCVPQMLVFLRVIGGLFVLVAVFQIISLVIYPVKYTQTFN

Parental  LHANP-AVTYIYNWAYGFGWAATIILIGCAFFFCCLPNYEDDLLGNAKPRYFYTSA
          L.A.P.AVTYIYNW.YGFGWAATIILI.CAFF..CLPN.EDDLLGN.KP..FYTSA
Retrocopy LQASP>AVTYIYNWPYGFGWAATIILISCAFFCYCLPNNEDDLLGNTKPKDFYTSA

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	1.34 RPM	2.91 RPM
SRP007412_brain_prefrontal_cortex	1.82 RPM	1.90 RPM
SRP007412_cerebellum	1.74 RPM	5.30 RPM
SRP007412_heart	1.12 RPM	49.88 RPM
SRP007412_kidney	1.29 RPM	24.88 RPM
SRP007412_liver	0.75 RPM	62.78 RPM
SRP007412_testis	0.53 RPM	5.01 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2156 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2156 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2156 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1523
Gorilla gorilla	retro_ggor_1165
Pongo abelii	retro_pabe_1267

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020097	1 retrocopy	retro_btau_165,
Callithrix jacchus	ENSCJAG00000019024	1 retrocopy	retro_cjac_3992,
Homo sapiens	ENSG00000112378	2 retrocopies	retro_hsap_1523, retro_hsap_2901,
Gorilla gorilla	ENSGGOG00000028340	1 retrocopy	retro_ggor_1165,
Macropus eugenii	ENSMEUG00000004872	1 retrocopy	retro_meug_845,
Microcebus murinus	ENSMICG00000013979	1 retrocopy	retro_mmur_353,
Myotis lucifugus	ENSMLUG00000001473	1 retrocopy	retro_mluc_2287,
Macaca mulatta	ENSMMUG00000000997	1 retrocopy	retro_mmul_2156 ,
Macaca mulatta	ENSMMUG00000004530	1 retrocopy	retro_mmul_1399,
Nomascus leucogenys	ENSNLEG00000014930	2 retrocopies	retro_nleu_1934, retro_nleu_631,
Oryctolagus cuniculus	ENSOCUG00000004238	1 retrocopy	retro_ocun_170,
Otolemur garnettii	ENSOGAG00000011669	1 retrocopy	retro_ogar_631,
Pongo abelii	ENSPPYG00000017043	3 retrocopies	retro_pabe_1267, retro_pabe_2400, retro_pabe_2416,