RetrogeneDB ID: retro_ptro_851

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 13:19079005..19079826(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ESRRA
• Ensembl ID: ENSPTRG00000003833
• Aliases: None
• Description: Estrogen-related receptor alpha [Source:UniProtKB/TrEMBL;Acc:K7DJ98]

Sequence

>retro_ptro_851
GGAGCGCGCCTGGACCGCGTCTGGGGTGGGCGGGAGAAGTACAAGTGGCGCCAGAGGTGGACCCGCTGCCCTTCCCGGAC
CCCTTCCCTGCTGGGCGCCTGGCAGTCGCTGGAGGCCCCTGGACGACAGGCCCAGTGAATGCGCTGGTGTCTCATCTGCT
GGTGGTTGAGCCTGAGAAGCTCTATGCCTTGCCCGACCCTGCTGGCCCTGATGGGCACCTTTCAGCCGTGGCTACCCTCT
GTGACCTCTTTGACCGAGAGATCGTGGTCACCATCAGCTGGGCCAAGAGCATCCCAGGCTTCTCATCGCTGTCGCTGTCT
GACCAGATGTCAGTACTGCAGAGCGTGTGGATGGAGGTGCTGGTGCCGGGTGTGGCCCAGCGCTCACTGCCACTGCAGGA
TGAGCTGGCCTTTGCTGAGGACTTAGTCCTGGATGAAGAGGGGGCACGGGCAGCTGGCCTGGGGGAACTGGGGGCTGCCC
TGCTGCAACTGGTGCGGCGGCTGCAGGCCCTGCGGCTGGAGCGAGGGGAGTACGTTCTACTGAAGGCCCTGGCCCTTGCC
AATTCAGACTCTGTGCCCATCGAAGATGCCGAGGCTGTGGAGCAGCTGCCAGAAGCTCTGCACGAGGCCCTGCTGGAGTA
TGAAGCCGGCCGGGCTGACCCCGGTGGGGGTGCTGAGCAGCTGCCAGGCAGGCTGCTGCTCACGCCACCGCTCTTCTGCC
AGACAGCGAGCAAAGTGCTGGCCCATTTCTATGGGGTGAAGCTGGAGGGCAAGGTGCCCATGCACAAGCTGTTCTTGGAG
ATGCTCGAGGCCATGATGGAC

Alignment

ORF - retro_ptro_851 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.61 %
• Parental protein coverage: 65.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GVRLDRVRGGRQKYKRR-PEVDPLPFPGPFPAGPLAVAGGPRKTAAPVNALVSHLLVVEPEKLYAMPDPA
          G.RLDRV.GGR.KYK.R.PEVDPLPFP.PFPAG.LAVAGGP..T..PVNALVSHLLVVEPEKLYA.PDPA
Retrocopy GARLDRVWGGREKYKWR<PEVDPLPFPDPFPAGRLAVAGGPW-TTGPVNALVSHLLVVEPEKLYALPDPA

Parental  GPDGHLPAVATLCDLFDREIVVTISWAKSIPGFSSLSLSDQMSVLQSVWMEVLVLGVAQRSLPLQDELAF
          GPDGHL.AVATLCDLFDREIVVTISWAKSIPGFSSLSLSDQMSVLQSVWMEVLV.GVAQRSLPLQDELAF
Retrocopy GPDGHLSAVATLCDLFDREIVVTISWAKSIPGFSSLSLSDQMSVLQSVWMEVLVPGVAQRSLPLQDELAF

Parental  AEDLVLDEEGARAAGLGELGAALLQLVRRLQALRLEREEYVLLKALALANSDSVHIEDAEAVEQLREALH
          AEDLVLDEEGARAAGLGELGAALLQLVRRLQALRLER.EYVLLKALALANSDSV.IEDAEAVEQL.EALH
Retrocopy AEDLVLDEEGARAAGLGELGAALLQLVRRLQALRLERGEYVLLKALALANSDSVPIEDAEAVEQLPEALH

Parental  EALLEYEAGRAGPGGGAERRRAGRLLLTLPLLRQTAGKVLAHFYGVKLEGKVPMHKLFLEMLEAMMD
          EALLEYEAGRA.PGGGAE....GRLLLT.PL..QTA.KVLAHFYGVKLEGKVPMHKLFLEMLEAMMD
Retrocopy EALLEYEAGRADPGGGAE-QLPGRLLLTPPLFCQTASKVLAHFYGVKLEGKVPMHKLFLEMLEAMMD

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_prefrontal_cortex	0.07 RPM	42.90 RPM
SRP007412_cerebellum	0.00 RPM	34.59 RPM
SRP007412_heart	0.03 RPM	48.73 RPM
SRP007412_kidney	0.00 RPM	125.48 RPM
SRP007412_liver	0.00 RPM	67.60 RPM
SRP007412_testis	0.11 RPM	3.69 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_851 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_851 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_851 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1237
Gorilla gorilla	retro_ggor_970

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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 ,