RetrogeneDB ID: retro_ggor_2908

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: X:54730702..54730996(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS18C
• Ensembl ID: ENSGGOG00000008603
• Aliases: None
• Description: None

Sequence

>retro_ggor_2908
GCTATGGTTGCTGTTTGCGGTGGTCTAGGGAGGAAGAAGTTGACACACCTGGTAACGGCTGCTGTCAGCCTTACACATCC
TGGGACTCCCATGGTGCTTTCCAGAAGGGGTTATTCACAATATAAACAGGTATCCAGCATTGAGGACCTGCCCAGTCCAA
TGGAAAACCCTTATAAAGAATCTCTTAAGAAATGTGTCTTGTGTGGAAAGCATGTAAATTAGAAGAATGCACAGCTTTTG
TCCCAGTTTGTTTCTCCATTTACTGGATGCATTTATGGAAGGCACGTTACAGGT

Alignment

ORF - retro_ggor_2908 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.37 %
• Parental protein coverage: 78.69 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AMVAVCGGLRRKKLTHLVTAAVSLTHPGTQTVLWRRGCSQ--QVSSNEDLPISMENPYKEPLKKCILCGK
          AMVAVCGGL.RKKLTHLVTAAVSLTHPGT..VL.RRG.SQ..QVSS.EDLP..MENPYKE.LKKC.LCGK
Retrocopy AMVAVCGGLGRKKLTHLVTAAVSLTHPGTPMVLSRRGYSQYKQVSSIEDLPSPMENPYKESLKKCVLCGK

Parental  HVDYKNVQLCGKKQKEITKAIKRAQIMG
          HV..KN.QL........T..I......G
Retrocopy HVN*KNAQLLSQFVSPFTGCIYGRHVTG

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	1.63 RPM	9.97 RPM
SRP007412_cerebellum	1.50 RPM	5.44 RPM
SRP007412_heart	0.44 RPM	3.85 RPM
SRP007412_kidney	3.07 RPM	14.43 RPM
SRP007412_liver	2.11 RPM	9.36 RPM
SRP007412_testis	2.49 RPM	10.26 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_2908 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2908 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4684
Pongo abelii	retro_pabe_70
Macaca mulatta	retro_mmul_2494

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018155	3 retrocopies	retro_btau_1386, retro_btau_309, retro_btau_502,
Callithrix jacchus	ENSCJAG00000005286	3 retrocopies	retro_cjac_1419, retro_cjac_234, retro_cjac_3970,
Cavia porcellus	ENSCPOG00000009198	1 retrocopy	retro_cpor_178,
Dasypus novemcinctus	ENSDNOG00000018326	2 retrocopies	retro_dnov_1030, retro_dnov_152,
Homo sapiens	ENSG00000163319	5 retrocopies	retro_hsap_1540, retro_hsap_2597, retro_hsap_4019, retro_hsap_4684, retro_hsap_969,
Gorilla gorilla	ENSGGOG00000008603	2 retrocopies	retro_ggor_1173, retro_ggor_2908 ,
Macropus eugenii	ENSMEUG00000010972	2 retrocopies	retro_meug_104, retro_meug_1113,
Myotis lucifugus	ENSMLUG00000017057	1 retrocopy	retro_mluc_2360,
Mus musculus	ENSMUSG00000016833	2 retrocopies	retro_mmus_1546, retro_mmus_2127,
Nomascus leucogenys	ENSNLEG00000009119	4 retrocopies	retro_nleu_111, retro_nleu_1614, retro_nleu_2722, retro_nleu_3010,
Ochotona princeps	ENSOPRG00000004113	2 retrocopies	retro_opri_1041, retro_opri_966,
Pongo abelii	ENSPPYG00000025867	2 retrocopies	retro_pabe_1276, retro_pabe_70,
Pan troglodytes	ENSPTRG00000016233	3 retrocopies	retro_ptro_1039, retro_ptro_1521, retro_ptro_3113,
Pteropus vampyrus	ENSPVAG00000006439	2 retrocopies	retro_pvam_1326, retro_pvam_1412,
Rattus norvegicus	ENSRNOG00000002178	3 retrocopies	retro_rnor_2264, retro_rnor_2265, retro_rnor_477,
Sarcophilus harrisii	ENSSHAG00000007084	1 retrocopy	retro_shar_718,
Ictidomys tridecemlineatus	ENSSTOG00000007989	1 retrocopy	retro_itri_1231,
Tupaia belangeri	ENSTBEG00000012505	3 retrocopies	retro_tbel_1755, retro_tbel_4724, retro_tbel_508,
Tarsius syrichta	ENSTSYG00000012924	1 retrocopy	retro_tsyr_649,
Tursiops truncatus	ENSTTRG00000004897	2 retrocopies	retro_ttru_144, retro_ttru_1721,