RetrogeneDB ID: retro_ptro_2017

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:132442334..132443169(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EEF1G
• Ensembl ID: ENSPTRG00000003768
• Aliases: None
• Description: eukaryotic translation elongation factor 1 gamma [Source:HGNC Symbol;Acc:3213]

Sequence

>retro_ptro_2017
CTGGCTGACATAGTAGTTTTCTGCACCCTGTTGTGGCTCTATAAGCAGGTTCTGGAGCCTTCTTCCTGCCAGGCCTTTCC
CAATACCAACTGCTGGTTCCTCACCTGCATTAACCAGCCCCAGTTCAGGGCTGTCTTAGGGAAGGTGAAACTGTCTGTGA
ACATGACCCAGTTTGATGCTAAAAAGCTTGCAGAAAGCCAGCCTGAAAAAGACACCCCATGGAAAGGGAAAGGTTCACGG
GAAAATAAGCAGCAGCCCCAAGCTGAGCGGAAGGAGGAGAAAAAGGCAGCTGCCCCTGCTCCTGAGGAGGAGATGGACGA
ATGTGAGCAGGTGCTGGCTGCTGAGCTCAAGGTCAAAGACCTCTTCGCTTACTTGCTCAAGAGTACCTTTGTGTTGGATG
AATTTAAGCGCAAGTACTCCAACGAGGACACGCTCTCTGTGGTGCTGCCCTATTTCTGGGAGCACTTTGATAAGGATGGC
TGGTTCCTGTGGTACTCACAATATCGCTTTCCTAAAGAACTCACTCAGACCTTTATACTTGCAATCTCATCACTGGAATG
TTCAAGCGACTGGACAAGCTGAGGAAGATGACTTTGCCAGTGTCATCCTCTTTGGAACCAACAACAGTAGCTCTATTTCT
GGAGTCTGAGGCTTCTGAGGCCAGGAGCTTGCCTTTCTGCTGAGTCCAGATTGGCAGATGGACTACCAGTCATACACATG
GCAAAAACCGGCTCCTGGCAGCGACGAGCCCCAGACCCTGGTTGGAGCGTAGTTTTCCTGGGAGGAGGGTTTCCAGAATA
TGGGCAGAGCCTTCATTCAGGGTGAGATTGTCAAG

Alignment

ORF - retro_ptro_2017 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.07 %
• Parental protein coverage: 57.29 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LADITVVCTLLWLYKQVLEPSFRQAFPNTNRWFLTCINQPQFRAVLGEVKLCEKMAQFDAKKFAETQPKK
          LADI.V.CTLLWLYKQVLEPS..QAFPNTN.WFLTCINQPQFRAVLG.VKL...M.QFDAKK.AE.QP.K
Retrocopy LADIVVFCTLLWLYKQVLEPSSCQAFPNTNCWFLTCINQPQFRAVLGKVKLSVNMTQFDAKKLAESQPEK

Parental  DTPRKEKGSREEKQKPQAERKEEKKAAAPAPEEEMDECEQALAAEPKAKDPFAHLPKSTFVLDEFKRKYS
          DTP.K.KGSRE.KQ.PQAERKEEKKAAAPAPEEEMDECEQ.LAAE.K.KD.FA.L.KSTFVLDEFKRKYS
Retrocopy DTPWKGKGSRENKQQPQAERKEEKKAAAPAPEEEMDECEQVLAAELKVKDLFAYLLKSTFVLDEFKRKYS

Parental  NEDTLSVALPYFWEHFDKDGWSLWYSEYRFPEELTQTFM-SCNLITGMFQRLDKLRK-NAFASVILFGTN
          NEDTLSV.LPYFWEHFDKDGW.LWYS.YRFP.ELTQTF...CNLITGMF.RLDKLRK...FASVILFGTN
Retrocopy NEDTLSVVLPYFWEHFDKDGWFLWYSQYRFPKELTQTFI<TCNLITGMFKRLDKLRK<DDFASVILFGTN

Parental  NSSSISGVWVFRGQELAFPLSPDWQVDYESYTWRKLDPGSEETQTLVREYFSWEGAFQHVGKAFNQGKIF
          NSSSISGV..F.GQELAF.LSPDWQ.DY.SYTW.K..PGS.E.QTLV...FSWE..FQ..G.AF.QG.I.
Retrocopy NSSSISGV*GF*GQELAFLLSPDWQMDYQSYTWQKPAPGSDEPQTLVGA*FSWEEGFQNMGRAFIQGEIV

Parental  K
          K
Retrocopy K

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	195.55 RPM
SRP007412_cerebellum	0.04 RPM	228.07 RPM
SRP007412_heart	0.00 RPM	290.06 RPM
SRP007412_kidney	0.03 RPM	641.01 RPM
SRP007412_liver	0.03 RPM	271.89 RPM
SRP007412_testis	0.11 RPM	237.32 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2017 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2017 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2017 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2982
Gorilla gorilla	retro_ggor_2065
Macaca mulatta	retro_mmul_1905

---

Parental genes homology:

Parental genes homology involve 26 parental genes, and 69 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006745	1 retrocopy	retro_amel_772,
Bos taurus	ENSBTAG00000011843	1 retrocopy	retro_btau_1600,
Canis familiaris	ENSCAFG00000015834	6 retrocopies	retro_cfam_1241, retro_cfam_1398, retro_cfam_1862, retro_cfam_478, retro_cfam_638, retro_cfam_653,
Callithrix jacchus	ENSCJAG00000018949	6 retrocopies	retro_cjac_1464, retro_cjac_1770, retro_cjac_1942, retro_cjac_3147, retro_cjac_841, retro_cjac_874,
Equus caballus	ENSECAG00000014334	1 retrocopy	retro_ecab_419,
Erinaceus europaeus	ENSEEUG00000001231	1 retrocopy	retro_eeur_575,
Homo sapiens	ENSG00000254772	4 retrocopies	retro_hsap_2778, retro_hsap_2982, retro_hsap_3906, retro_hsap_4744,
Latimeria chalumnae	ENSLACG00000014700	1 retrocopy	retro_lcha_82,
Loxodonta africana	ENSLAFG00000003339	1 retrocopy	retro_lafr_381,
Myotis lucifugus	ENSMLUG00000000342	1 retrocopy	retro_mluc_1110,
Macaca mulatta	ENSMMUG00000006598	5 retrocopies	retro_mmul_1447, retro_mmul_1905, retro_mmul_2528, retro_mmul_736, retro_mmul_802,
Monodelphis domestica	ENSMODG00000007691	1 retrocopy	retro_mdom_68,
Mustela putorius furo	ENSMPUG00000013942	2 retrocopies	retro_mputfur_427, retro_mputfur_944,
Mus musculus	ENSMUSG00000071644	7 retrocopies	retro_mmus_1447, retro_mmus_1839, retro_mmus_2350, retro_mmus_2765, retro_mmus_3080, retro_mmus_425, retro_mmus_989,
Nomascus leucogenys	ENSNLEG00000003528	2 retrocopies	retro_nleu_1510, retro_nleu_681,
Oryctolagus cuniculus	ENSOCUG00000020959	3 retrocopies	retro_ocun_1693, retro_ocun_369, retro_ocun_693,
Otolemur garnettii	ENSOGAG00000000827	1 retrocopy	retro_ogar_1344,
Ochotona princeps	ENSOPRG00000014563	1 retrocopy	retro_opri_814,
Pongo abelii	ENSPPYG00000029434	5 retrocopies	retro_pabe_2237, retro_pabe_2378, retro_pabe_2409, retro_pabe_2473, retro_pabe_3690,
Pan troglodytes	ENSPTRG00000003768	3 retrocopies	retro_ptro_1879, retro_ptro_2017 , retro_ptro_3159,
Pteropus vampyrus	ENSPVAG00000003440	1 retrocopy	retro_pvam_1239,
Rattus norvegicus	ENSRNOG00000020075	8 retrocopies	retro_rnor_1312, retro_rnor_2126, retro_rnor_2235, retro_rnor_2269, retro_rnor_2468, retro_rnor_2617, retro_rnor_2928, retro_rnor_979,
Sorex araneus	ENSSARG00000011232	1 retrocopy	retro_sara_718,
Sus scrofa	ENSSSCG00000013064	1 retrocopy	retro_sscr_164,
Ictidomys tridecemlineatus	ENSSTOG00000002851	2 retrocopies	retro_itri_852, retro_itri_886,
Tursiops truncatus	ENSTTRG00000002459	3 retrocopies	retro_ttru_1082, retro_ttru_1544, retro_ttru_1603,