RetrogeneDB ID: retro_cjac_1942

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:94268339..94269084(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EEF1G
• Ensembl ID: ENSCJAG00000018949
• Aliases: None
• Description: eukaryotic translation elongation factor 1 gamma [Source:HGNC Symbol;Acc:3213]

Sequence

>retro_cjac_1942
AAGGCCCTCATTGCTGCTCAGTACAGTGGGGCTCAGGTCCACCAGCTCTCCACACCACCCCACTTCCACTTTGGCCAAAC
CAACCACACCCCTGAATTTCTCCACGAATTTCCTGTTGGCAAGTTTCCAGCATTTGAGGGTGATGATAGATTCTGTGTGT
TTCAGAGCAGTGCCATTGCCTACTATGTGAGCAATGACGAGCTGTGGGGAAGTATTCCAGAGGCAGCAGTCCAGATGGTG
CAGTGGGTGAACTTTGCTGATAGCGACATAGTACCCCCAGCCAGTACCTGGGTGTTCCCCACCTTGGGCATCACGTATCA
CAACAAACAGGCCACTGAGAATGCAAAAGAGGAAGTGAGGTGAATTGTGGGGCTGCTGGATGGTCGGTCACTGGAAGACG
AGGATTTTTCTGGTGGGCAAACAAGTGACATTGGCTGACATCACCATTATCTGCACTCTGTTGTGACTTTATAAACAGGT
CCTAGAGCCTTCTTTCTGCCAGGCTGTTCCCAATACCAACCACTGGTTCCTCACCTGCATTAACCAGCCTCAGTTCCAGA
CTGTCTTGGGGGAAGTGAAACTGTGTGAGAAGATGGCCCAGTTTGATGCTAAAAAGTTGGCAGAGAGCCAACCTAAAAGG
GACACACCACGGAAAGAGAAGTGTTCATGGGAAGAGAAGCAGCAGCCCCAGGCTGAGCAGAAGGAGGAGAAAAAGGCAGC
TGCCCCTGCAGCTCCTGAGGAGGAG

Alignment

ORF - retro_cjac_1942 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.93 %
• Parental protein coverage: 56.29 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KALIAAQYSGAQVRVLSAPPHFHFGQTNRTPEFLRKFPAGKVPAFEGDDGFCVFESNAIAYYVSNEELRG
          KALIAAQYSGAQV..LS.PPHFHFGQTN.TPEFL..FP.GK.PAFEGDD.FCVF.S.AIAYYVSN.EL.G
Retrocopy KALIAAQYSGAQVHQLSTPPHFHFGQTNHTPEFLHEFPVGKFPAFEGDDRFCVFQSSAIAYYVSNDELWG

Parental  STPEAAAQVVQWVSFADSDIVPPASTWVFPTLGIMHHNKQATENAKEEVRRILGLLDAH-LKTRTF-LVG
          S.PEAA.Q.VQWV.FADSDIVPPASTWVFPTLGI..HNKQATENAKEEVR.I.GLLD...L....F.LVG
Retrocopy SIPEAAVQMVQWVNFADSDIVPPASTWVFPTLGITYHNKQATENAKEEVR*IVGLLDGRSLEDEDF>LVG

Parental  ERVTLADITVVCTLLWLYKQVLEPSFRQAFPNTNRWFLTCINQPQFRAVLGEVKLCEKMAQFDAKKFAES
          ..VTLADIT..CTLL.LYKQVLEPSF.QA.PNTN.WFLTCINQPQF..VLGEVKLCEKMAQFDAKK.AES
Retrocopy KQVTLADITIICTLL*LYKQVLEPSFCQAVPNTNHWFLTCINQPQFQTVLGEVKLCEKMAQFDAKKLAES

Parental  QPKRDTPRKEKGSREEKQKPQAERKEEKKAAAP-APEEE
          QPKRDTPRKEK.S.EEKQ.PQAE.KEEKKAAAP.APEEE
Retrocopy QPKRDTPRKEKCSWEEKQQPQAEQKEEKKAAAPAAPEEE

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
SRP051959_colon	0.00 RPM	266.83 RPM
SRP051959_heart	0.00 RPM	225.85 RPM
SRP051959_kidney	0.09 RPM	205.91 RPM
SRP051959_liver	0.06 RPM	203.24 RPM
SRP051959_lung	0.08 RPM	189.37 RPM
SRP051959_lymph_node	0.00 RPM	312.64 RPM
SRP051959_skeletal_muscle	0.09 RPM	248.58 RPM
SRP051959_spleen	0.06 RPM	287.10 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1942 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1942 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1942 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 50 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,
Latimeria chalumnae	ENSLACG00000014700	1 retrocopy	retro_lcha_82,
Loxodonta africana	ENSLAFG00000003339	1 retrocopy	retro_lafr_381,
Myotis lucifugus	ENSMLUG00000000342	1 retrocopy	retro_mluc_1110,
Monodelphis domestica	ENSMODG00000007691	1 retrocopy	retro_mdom_68,
Mustela putorius furo	ENSMPUG00000013942	2 retrocopies	retro_mputfur_427, retro_mputfur_944,
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,
Tursiops truncatus	ENSTTRG00000002459	3 retrocopies	retro_ttru_1082, retro_ttru_1544, retro_ttru_1603,