RetrogeneDB ID: retro_ggor_1351

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 17:55494162..55494568(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRDX4
• Ensembl ID: ENSGGOG00000026790
• Aliases: None
• Description: None

Sequence

>retro_ggor_1351
GTCTATTTTTTCCTTGATTTTACATGTGTGTGTCCAACTAAAATAATCAATTTTAGTGACAAAATTGAGAACTTAGACCA
CTAAACACTGAAGTGATACCATGCCTTGCTGACTCACAGTTTACCCATTTAGTATGAAGTCCCGCCCCTCGCAAACAAAG
AGGACTGGAGCCCGGGGAAAATTTCATTTCTTTCAGATTTTATCCATCAGATCTCAAAGTGCTATGGTGATGTATCTGGA
GAATTCAGGCCACAGTCTTAGAGGTTTCTTCACTATTGATGAAAAAGGAATCCAAAGGTAGTTTAGAATGGATGACCCTC
CTGTCAGCAGAGTAGTAAATAAAATACTGTATTGGGGTCAAGTGTCCCTGTACACTGACCAGTATGGAAAAGTCTATGCT
GTTGGA

Alignment

ORF - retro_ggor_1351 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.29 %
• Parental protein coverage: 50.55 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VFFFYPLDFTFVCPTEIIAFGDRLE-EFRSINTEVVACSVDSQFTHLAWINTPRRQGGL-GPIRIPLLSD
          V.FF..LDFT.VCPT.II.F.D..E.E.R..NTEV..C..DSQFTHL.....PR.Q.GL..P..I..LSD
Retrocopy VYFF--LDFTCVCPTKIINFSDKIE<ELRPLNTEVIPCLADSQFTHLV*SPAPRKQRGL>SPGKISFLSD

Parental  LTHQISKDYG-VYLEDSGHTLRGLFIIDDKGILRQITLNDLPVGRSVDETLRLVQAFQYTDKHGEVCPAG
          ..HQISK.YG..YLE.SGH.LRG.F.ID.KGI.R.....D.PV.R.V...L...Q...YTD..G.V...G
Retrocopy FIHQISKCYG>MYLENSGHSLRGFFTIDEKGIQR*FRMDDPPVSRVVNKILYWGQVSLYTDQYGKVYAVG

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	4.94 RPM
SRP007412_cerebellum	0.00 RPM	6.30 RPM
SRP007412_heart	0.00 RPM	5.94 RPM
SRP007412_kidney	0.00 RPM	17.30 RPM
SRP007412_liver	0.00 RPM	67.05 RPM
SRP007412_testis	0.00 RPM	44.65 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_1351 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1351 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3165
Macaca mulatta	retro_mmul_2001
Equus caballus	retro_ecab_576

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006165	1 retrocopy	retro_btau_439,
Cavia porcellus	ENSCPOG00000004185	1 retrocopy	retro_cpor_353,
Equus caballus	ENSECAG00000010085	1 retrocopy	retro_ecab_576,
Homo sapiens	ENSG00000123131	1 retrocopy	retro_hsap_3165,
Gorilla gorilla	ENSGGOG00000025089	3 retrocopies	retro_ggor_2366, retro_ggor_2833, retro_ggor_923,
Gorilla gorilla	ENSGGOG00000026364	1 retrocopy	retro_ggor_986,
Gorilla gorilla	ENSGGOG00000026790	1 retrocopy	retro_ggor_1351 ,
Myotis lucifugus	ENSMLUG00000004904	2 retrocopies	retro_mluc_2347, retro_mluc_2619,
Macaca mulatta	ENSMMUG00000021366	1 retrocopy	retro_mmul_2001,
Tupaia belangeri	ENSTBEG00000004454	5 retrocopies	retro_tbel_2164, retro_tbel_2467, retro_tbel_2522, retro_tbel_2811, retro_tbel_2978,
Tarsius syrichta	ENSTSYG00000000602	1 retrocopy	retro_tsyr_404,
Tursiops truncatus	ENSTTRG00000012368	1 retrocopy	retro_ttru_547,