RetrogeneDB ID: retro_ggor_1974

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 3:143154254..143154784(-)
• Located in intron of: ENSGGOG00000007872

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL8
• Ensembl ID: ENSGGOG00000008164
• Aliases: None
• Description: None

Sequence

>retro_ggor_1974
AAGGGCATTCACACGGGCCAGTTTGTGTATTGCGGCAAGAAGGCCCAGCTCAACATTGGCAGTGTGCTCCCTGTGGGCAC
CATGCCTGAGGGTATGATCGTGTGCTGCCTGGAGGAGAAACCTGGAGGCCGTAGCAAGCTGTCCTGGGCATCAGGGAACG
ATGCCACTGCTGTCTCCCACAGCCCTGAGACCTAGAAGACCTGTGTGAAGCTGCCCTCTGGCTCCAAGAAGGTTATCTCC
TCAGCCAACAGAGCTGTGGTTGGTGTGGTGGCTGGAGGTGGCCGAACTGACAAACCCATCTTGAAGGCTTGCCAAGCCTA
CCACAAATATAAGGCAAAGAGGAACTGGTGGCCACGAGTATGGGATGTGGCCATGAACCCTATGGAGCATCCTTTTGGAG
GTGGCAACCACCAGCACATCGGCATCCCCTCTGCCATCTCAGAGATGACCCTGCTGGCTGCAAAATGGGTCTCATTGCTG
CCTGCCAGACTGGACGTCTCTGGGGAACCAAGACTGCAGGAGAAAGAGAA

Alignment

ORF - retro_ggor_1974 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.46 %
• Parental protein coverage: 68.87 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EGIHTGQFVYCGKKAQLNIGNVLPVGTMPEGTIVCCLEEKPGDRGKLARASGNYATVISHNPETKKTRVK
          .GIHTGQFVYCGKKAQLNIG.VLPVGTMPEG.IVCCLEEKPG.R.KL..ASGN.AT..SH.PET.KT.VK
Retrocopy KGIHTGQFVYCGKKAQLNIGSVLPVGTMPEGMIVCCLEEKPGGRSKLSWASGNDATAVSHSPET*KTCVK

Parental  LPSGSKKVISSANRAVVGVVAGGGRIDKPILKAGRAYHKYKAKRNCWPRVRGVAMNPVEHPFGGGNHQHI
          LPSGSKKVISSANRAVVGVVAGGGR.DKPILKA..AYHKYKAKRN.WPRV..VAMNP.EHPFGGGNHQHI
Retrocopy LPSGSKKVISSANRAVVGVVAGGGRTDKPILKACQAYHKYKAKRNWWPRVWDVAMNPMEHPFGGGNHQHI

Parental  GKPSTIR-RDAPAGRKVGLIAARRTGRLRGTKTVQEKE
          G.PS.I..RD.PAG.K.GLIAA..TGRL.GTKT..E.E
Retrocopy GIPSAIS<RDDPAGCKMGLIAACQTGRLWGTKTAGERE

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	0.10 RPM	447.75 RPM
SRP007412_cerebellum	0.04 RPM	442.60 RPM
SRP007412_heart	0.09 RPM	482.49 RPM
SRP007412_kidney	0.08 RPM	638.03 RPM
SRP007412_liver	0.03 RPM	619.22 RPM
SRP007412_testis	0.10 RPM	373.27 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_1974 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1974 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2851
Pan troglodytes	retro_ptro_1931
Macaca mulatta	retro_mmul_1470

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000017933	1 retrocopy	retro_acar_31,
Bos taurus	ENSBTAG00000026327	1 retrocopy	retro_btau_96,
Dasypus novemcinctus	ENSDNOG00000009300	2 retrocopies	retro_dnov_2505, retro_dnov_503,
Gorilla gorilla	ENSGGOG00000008164	1 retrocopy	retro_ggor_1974 ,
Macaca mulatta	ENSMMUG00000013379	2 retrocopies	retro_mmul_1470, retro_mmul_1531,
Mustela putorius furo	ENSMPUG00000006022	1 retrocopy	retro_mputfur_1517,
Mus musculus	ENSMUSG00000003970	2 retrocopies	retro_mmus_2004, retro_mmus_2112,
Oryctolagus cuniculus	ENSOCUG00000024716	1 retrocopy	retro_ocun_146,
Pan troglodytes	ENSPTRG00000020716	1 retrocopy	retro_ptro_1931,
Rattus norvegicus	ENSRNOG00000048523	2 retrocopies	retro_rnor_122, retro_rnor_239,