RetrogeneDB ID: retro_ggor_222

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 1:20236404..20236874(+)
• Located in intron of: ENSGGOG00000007347

Retrocopy information

• Ensembl ID: ENSGGOG00000023653
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPS14
• Ensembl ID: ENSGGOG00000024593
• Aliases: None
• Description: None

Sequence

>retro_ggor_222
TGGAGACGACGTGCAGAAATGGCACCTGGAAAGGGGAAGGAAAAGAAGGAAGAACAGGTCATCAACCTCGGACCTCAGGT
GGCTGAAGGGGAGAATGTATTTGGTGTCTGCCATGTCTTTGCATCCTTCAATGACACTTTTGTCCATGTCACGGATCTTT
CTGGCAAACAAACCATCTGCCGTGTGACTGGTGGGATGAAGGTGAAGGCAGACCGAGATGAATCCTCGCCATATGCTGCT
ATGTTGACCACCCAGGATGTGGCCCAGAGGTGCAAGGAGCTGGGTATCATTGCCCTACACATCGAACTCCAGGCCACAGG
AGGAAATAGGACCAAGACCCTTGGACCTGGGGCCCAGTCGGCCCTCAGAGCCCTTGCCTGCTCGGGTATGAAGATCGGGA
GGATTGAGGACGTCACCCCCATCCCCTCTGACAGCACTCTCAGGAAGGGGGTCGCCGTGGTCACCGTCTG

Alignment

ORF - retro_ggor_222 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.51 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  WRQRAEMAPRKGKEKKEEQVISLGPQVAEGENVFGVCHIFASFNDTFVHVTDLSGKETICRVTGGMKVKA
          WR.RAEMAP.KGKEKKEEQVI.LGPQVAEGENVFGVCH.FASFNDTFVHVTDLSGK.TICRVTGGMKVKA
Retrocopy WRRRAEMAPGKGKEKKEEQVINLGPQVAEGENVFGVCHVFASFNDTFVHVTDLSGKQTICRVTGGMKVKA

Parental  DRDESSPYAAMLAAQDVAQRCKELGITALHIKLRATGGNRTKTPGPGAQSALRALARSGMKIGRIEDVTP
          DRDESSPYAAML..QDVAQRCKELGI.ALHI.L.ATGGNRTKT.GPGAQSALRALA.SGMKIGRIEDVTP
Retrocopy DRDESSPYAAMLTTQDVAQRCKELGIIALHIELQATGGNRTKTLGPGAQSALRALACSGMKIGRIEDVTP

Parental  IPSDSTRRK-GGRRGRRL
          IPSDST.RK.GGRRG.RL
Retrocopy IPSDSTLRK<GGRRGHRL

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	0.43 RPM	190.33 RPM
SRP007412_cerebellum	0.63 RPM	150.38 RPM
SRP007412_heart	0.63 RPM	137.62 RPM
SRP007412_kidney	1.68 RPM	391.59 RPM
SRP007412_liver	2.00 RPM	366.68 RPM
SRP007412_testis	2.28 RPM	282.41 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_222 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_222 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_119
Pan troglodytes	retro_ptro_130
Pongo abelii	retro_pabe_494
Macaca mulatta	retro_mmul_358

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Parental genes homology:

Parental genes homology involve 28 parental genes, and 96 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000015004	1 retrocopy	retro_acar_201,
Ailuropoda melanoleuca	ENSAMEG00000004644	2 retrocopies	retro_amel_1390, retro_amel_524,
Bos taurus	ENSBTAG00000008570	2 retrocopies	retro_btau_1109, retro_btau_213,
Canis familiaris	ENSCAFG00000018094	2 retrocopies	retro_cfam_1589, retro_cfam_301,
Callithrix jacchus	ENSCJAG00000020981	1 retrocopy	retro_cjac_89,
Cavia porcellus	ENSCPOG00000024408	2 retrocopies	retro_cpor_253, retro_cpor_284,
Dipodomys ordii	ENSDORG00000007146	2 retrocopies	retro_dord_174, retro_dord_330,
Echinops telfairi	ENSETEG00000002899	6 retrocopies	retro_etel_1270, retro_etel_1358, retro_etel_1851, retro_etel_1995, retro_etel_293, retro_etel_967,
Homo sapiens	ENSG00000164587	8 retrocopies	retro_hsap_119, retro_hsap_1622, retro_hsap_268, retro_hsap_3001, retro_hsap_3113, retro_hsap_3232, retro_hsap_3495, retro_hsap_3789,
Gorilla gorilla	ENSGGOG00000024593	8 retrocopies	retro_ggor_1225, retro_ggor_2080, retro_ggor_2135, retro_ggor_2199, retro_ggor_222 , retro_ggor_2362, retro_ggor_2548, retro_ggor_316,
Latimeria chalumnae	ENSLACG00000016164	1 retrocopy	retro_lcha_12,
Loxodonta africana	ENSLAFG00000031195	2 retrocopies	retro_lafr_235, retro_lafr_67,
Macropus eugenii	ENSMEUG00000014907	1 retrocopy	retro_meug_619,
Microcebus murinus	ENSMICG00000002900	2 retrocopies	retro_mmur_1569, retro_mmur_433,
Myotis lucifugus	ENSMLUG00000013279	4 retrocopies	retro_mluc_1837, retro_mluc_205, retro_mluc_2464, retro_mluc_2485,
Macaca mulatta	ENSMMUG00000002848	5 retrocopies	retro_mmul_1921, retro_mmul_1983, retro_mmul_358, retro_mmul_570, retro_mmul_90,
Mustela putorius furo	ENSMPUG00000013776	1 retrocopy	retro_mputfur_127,
Nomascus leucogenys	ENSNLEG00000010366	1 retrocopy	retro_nleu_101,
Oryctolagus cuniculus	ENSOCUG00000011509	1 retrocopy	retro_ocun_128,
Otolemur garnettii	ENSOGAG00000000721	1 retrocopy	retro_ogar_286,
Procavia capensis	ENSPCAG00000015960	3 retrocopies	retro_pcap_198, retro_pcap_443, retro_pcap_73,
Pongo abelii	ENSPPYG00000015950	7 retrocopies	retro_pabe_1340, retro_pabe_2487, retro_pabe_2571, retro_pabe_2888, retro_pabe_3204, retro_pabe_401, retro_pabe_494,
Pelodiscus sinensis	ENSPSIG00000005922	1 retrocopy	retro_psin_33,
Pan troglodytes	ENSPTRG00000017418	8 retrocopies	retro_ptro_1086, retro_ptro_130, retro_ptro_2030, retro_ptro_2104, retro_ptro_2184, retro_ptro_224, retro_ptro_2367, retro_ptro_2570,
Rattus norvegicus	ENSRNOG00000018774	10 retrocopies	retro_rnor_1313, retro_rnor_1467, retro_rnor_1532, retro_rnor_1759, retro_rnor_1875, retro_rnor_1918, retro_rnor_2181, retro_rnor_228, retro_rnor_2728, retro_rnor_873,
Sorex araneus	ENSSARG00000014249	1 retrocopy	retro_sara_537,
Sarcophilus harrisii	ENSSHAG00000018052	3 retrocopies	retro_shar_380, retro_shar_381, retro_shar_503,
Tupaia belangeri	ENSTBEG00000006368	10 retrocopies	retro_tbel_1147, retro_tbel_1332, retro_tbel_1603, retro_tbel_1868, retro_tbel_202, retro_tbel_3517, retro_tbel_3619, retro_tbel_416, retro_tbel_519, retro_tbel_740,