RetrogeneDB ID: retro_mmul_1275

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 17:1856058..1856883(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ESRRA
• Ensembl ID: ENSMMUG00000017803
• Aliases: None
• Description: estrogen-related receptor alpha [Source:HGNC Symbol;Acc:3471]

Sequence

>retro_mmul_1275
GGAGTGCGCCTGGACCGCGTCCGGGGTGAGTGGCAGAAGTACAAGCAGCGGCCAGAGGTGGATCTGCTGCCCTTTCCGGG
CCCCTTCCCTGCTGGGCCCCTGGCAGTTGCTGGAGGCCCCCGGAAGACAGCCCCAGTCAATGTGCTGGTGTCTCATCTGC
TGGTGGTTGAGCCTGAGAAGCTCTATGCCATGCCTGACCCTGCTGGCCCTGATTGGCACCTCCCAGCCGTGGCTACCCTC
TGTGACCTCTTTGACTGAGAGATCGTGGTCACCATCAGCTGGGCCAAGAGCATCCCAGGCTTCTCATTGCTGTCGCTGTC
TGACCAGATGTCAGGACTGCAGAGCCTGTGGATGGAGTTGCTGGTGCCGGGTGTGGCCCAGCTCTCACTGCCACTGCAGG
ATGAGCTGGCCTTCGCTGAGGACTTAGTCCTGGATGAAGAGGGGGCACGGGCAGCTGGACTGGGGGAACGGGGGTCTGCC
CTGCTGCAACTGGTGCGGAGGCTGCAGGCCCTGCGGCTGGAGGGAGAGGAGTATGTTCTACTGAAGGCACTGGCCCTTGC
CAGTTCAAGCTGTGTGCACATCGAAGATGCCGAGGCTGTGGAGCAGCTGCTGGAAGCTCTGCACGAGGCCCTGCTGGAGT
ACGAAGCTGGCCGGGCTGGCACCGGAGAGGGTGCTGAGCCGTGCCGGGCAGGCAGGCTGCTGCTCACGCTACCGCTCCTC
CGCCAGACAGTGGGCAAAGTGCTGGCCCATTTCTATGGGGTGAAGCTGGAGGTCAAGGTGCCCGTGCACAAGCTGTTCTT
GGAGATGCTCGAGGCCATGATGGAC

Alignment

ORF - retro_mmul_1275 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.82 %
• Parental protein coverage: 65.17 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GVRLDRVRGGRQKYKRRPEVDPLPFPGPFPAGPLAVSGGPRKTAPVNALVSHLLVVEPEKLYAMPDPAGP
          GVRLDRVRG..QKYK.RPEVD.LPFPGPFPAGPLAV.GGPRKTAPVN.LVSHLLVVEPEKLYAMPDPAGP
Retrocopy GVRLDRVRGEWQKYKQRPEVDLLPFPGPFPAGPLAVAGGPRKTAPVNVLVSHLLVVEPEKLYAMPDPAGP

Parental  DGHLPAVATLCDLFDREIVVTISWAKSIPGFSSLSLSDQMSVLQSVWMEVLVLGVAQRSLPLQDELAFAE
          D.HLPAVATLCDLFD.EIVVTISWAKSIPGFS.LSLSDQMS.LQS.WME.LV.GVAQ.SLPLQDELAFAE
Retrocopy DWHLPAVATLCDLFD*EIVVTISWAKSIPGFSLLSLSDQMSGLQSLWMELLVPGVAQLSLPLQDELAFAE

Parental  DLVLDEEGARAAGLGELGAALLQLVRRLQALRLEREEYVLLKALALANSDSVHIEDAEAVEQLREALHEA
          DLVLDEEGARAAGLGE.G.ALLQLVRRLQALRLE.EEYVLLKALALA.S..VHIEDAEAVEQL.EALHEA
Retrocopy DLVLDEEGARAAGLGERGSALLQLVRRLQALRLEGEEYVLLKALALASSSCVHIEDAEAVEQLLEALHEA

Parental  LLEYEAGRAGPGGGAERRRAGRLLLTLPLLRQTAGKVLAHFYGVKLEGKVPMHKLFLEMLEAMMD
          LLEYEAGRAG.G.GAE..RAGRLLLTLPLLRQT.GKVLAHFYGVKLE.KVP.HKLFLEMLEAMMD
Retrocopy LLEYEAGRAGTGEGAEPCRAGRLLLTLPLLRQTVGKVLAHFYGVKLEVKVPVHKLFLEMLEAMMD

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	8.18 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	22.69 RPM
SRP007412_cerebellum	0.00 RPM	15.76 RPM
SRP007412_heart	0.00 RPM	34.27 RPM
SRP007412_kidney	0.00 RPM	31.45 RPM
SRP007412_liver	0.04 RPM	25.89 RPM
SRP007412_testis	0.04 RPM	4.82 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1275 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1275 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1275 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018030	3 retrocopies	retro_cjac_3845, retro_cjac_3982, retro_cjac_4023,
Echinops telfairi	ENSETEG00000000262	1 retrocopy	retro_etel_733,
Homo sapiens	ENSG00000173153	2 retrocopies	retro_hsap_1171, retro_hsap_1237,
Gorilla gorilla	ENSGGOG00000001333	1 retrocopy	retro_ggor_970,
Macaca mulatta	ENSMMUG00000017803	1 retrocopy	retro_mmul_1275 ,
Nomascus leucogenys	ENSNLEG00000004971	2 retrocopies	retro_nleu_2855, retro_nleu_2856,
Pongo abelii	ENSPPYG00000003107	1 retrocopy	retro_pabe_63,
Pan troglodytes	ENSPTRG00000003833	1 retrocopy	retro_ptro_851,