RetrogeneDB ID: retro_ggor_1915

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 3:13847083..13847678(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRR3
• Ensembl ID: ENSGGOG00000014604
• Aliases: None
• Description: None

Sequence

>retro_ggor_1915
CCAAATCCCACTGCAGCCTTTGCTGCCACCACAATGCCGAAATGAAAGAAGCAGAATCAGCACCAGCCCCCGCCACAGCA
GCAGCCCGCACTGCCCGAGAGGGAAAAGACTGGAGCTGACGAGGATGGGAGTCCCATCGGATCACCCAGCCTTCTTGAGC
CTCCCACCATGGCCATTGGAAAACCTGATGACCGTAAGTCAGCTCCTCACAGAGGTCTTCCAGGAGCAAGGGGACCACTG
ATTCTACCGCTGCTGAGCCTCCCACCTCCTCCTCAGGGTACAGGCCCAATGCCAGGAGGCCTTGGCCCCAGGCCTAGCCC
ATATGATTGTGGTTGGTGGGGAGTCAATGCTGAACCTCCTTTTCCGGCGCCAGGCCATGGGGGTCCCGCCAGGTGAAGCC
TTCACAGAGAACAGAGAAACCCTCAAAGGCTCGAAAGCCGGTCTCTTATCAAGAATACCAGCCCACTAGGATGACCCCCA
GGTTATGGAAGACAAATCCCACCACCCAGTCTGTGGACATTTTGCCAAAAAGGGCCACTGTCAATATGAGGACCTCTGTG
CCTTCCACCACCCAGGCATCAATAGCCCTCCTCTG

Alignment

ORF - retro_ggor_1915 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.5 %
• Parental protein coverage: 78.66 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PNPAAAIAADTMPKRKKQNQHQPPTQQQPPLPEREETGDEEDGSPIGPPSLLGPPPMANGKPGDPKSALH
          PNP.AA.AA.TMPK.KKQNQHQPP.QQQP.LPERE.TG..EDGSPIG.PSLL.PP.MA.GKP.D.KSA.H
Retrocopy PNPTAAFAATTMPK*KKQNQHQPPPQQQPALPEREKTGADEDGSPIGSPSLLEPPTMAIGKPDDRKSAPH

Parental  RGPPGSRGPLIPPLLSLPPPPWGRGPIRRGLGPRSSPYGRGWWGVNAEPPFPGPGH-GGPTRGSFHKEQR
          RG.PG.RGPLI.PLLSLPPPP.G.GP...GLGPR.SPY..GWWGVNAEPPFP.PGH.G.P....F..E.R
Retrocopy RGLPGARGPLILPLLSLPPPPQGTGPMPGGLGPRPSPYDCGWWGVNAEPPFPAPGH>GVPPGEAF-TENR

Parental  NPQRLKSWSLIKNTCPPKDDPQVMEDKSDRPVCRHFAKKGHCRYEDLCAFYHPGVNGPPL
          .........L........DDPQVMEDKS..PVC.HFAKKGHC.YEDLCAF.HPG.N.PPL
Retrocopy ETLKGSKAGLLSRIPAH*DDPQVMEDKSHHPVCGHFAKKGHCQYEDLCAFHHPGINSPPL

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	0.00 RPM	14.96 RPM
SRP007412_cerebellum	0.00 RPM	17.69 RPM
SRP007412_heart	0.00 RPM	2.63 RPM
SRP007412_kidney	0.00 RPM	7.69 RPM
SRP007412_liver	0.00 RPM	5.43 RPM
SRP007412_testis	0.10 RPM	8.08 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_1915 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1915 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1861
Pongo abelii	retro_pabe_2279

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000022770	1 retrocopy	retro_cpor_775,
Felis catus	ENSFCAG00000025918	2 retrocopies	retro_fcat_1094, retro_fcat_1698,
Gorilla gorilla	ENSGGOG00000014604	1 retrocopy	retro_ggor_1915 ,
Myotis lucifugus	ENSMLUG00000008758	1 retrocopy	retro_mluc_1567,
Macaca mulatta	ENSMMUG00000013893	1 retrocopy	retro_mmul_1431,
Nomascus leucogenys	ENSNLEG00000005104	1 retrocopy	retro_nleu_1548,
Otolemur garnettii	ENSOGAG00000004430	2 retrocopies	retro_ogar_1030, retro_ogar_1324,
Pongo abelii	ENSPPYG00000016409	1 retrocopy	retro_pabe_2279,
Pan troglodytes	ENSPTRG00000017929	1 retrocopy	retro_ptro_1861,
Sorex araneus	ENSSARG00000002747	2 retrocopies	retro_sara_143, retro_sara_9,
Ictidomys tridecemlineatus	ENSSTOG00000011829	1 retrocopy	retro_itri_126,
Tarsius syrichta	ENSTSYG00000000166	2 retrocopies	retro_tsyr_308, retro_tsyr_841,