RetrogeneDB ID: retro_mmul_1905

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 5:122231730..122232478(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.2624
• Ensembl ID: ENSMMUG00000006598
• Aliases: None
• Description: eukaryotic translation elongation factor 1 gamma [Source:RefSeq peptide;Acc:NP_001182509]

Sequence

>retro_mmul_1905
CTGGCTGACATCGCAGTTGTCTGCACTCTGATGTGGCTCTATAAGCAGGTCCTGGAGCCTTCTTTCTGCCAGGCCTTTCC
CAATACCAACACTGGTTCCTCAACTTCATTAACCAACCCCAATTCCGGACTGTCTTATGGAAGGTGAAACTGTCTGAGAA
CATGGCTCAGTTTGATGCTAAAAAGCTTGCAGAAAGCCAGTCTGAAAAAGACATCCCATGGAAAGGGAAAGGTTCACGGG
AAAGGAAGCAGTAGCTCCAGGCTGAGCGGAAGGAGGAGAAAAAGGCGGCTGCCCCCGCTCCTGAGGAGGAGATGGACGAA
CGTGAGCAGGTGCTGGCTGCTGAGCCCAAGGTCAAAGACTTCTTCGCTCACTTTCTCAGGAGTACCTTTGTTTTGGATGA
ATTTAAGCACAAGTACTCCAACGAGGACACACACTTTGTGGTGCTGCCCTATTTCTGGGAGCACTTTGATAAGGATGACT
GGTCCCTGTGGTAATCAGAATATCTCTTCCCTAAAGAACTCACTCAGACCTTTATGACTTGCAATCTCATCACTGGAATG
TTCAAGCGACTGGACAAGCTGAGGAAGATGCCTTTGCCAGTGTCATCCTCTTTGGAACCGACAAGGGCAGCTCTATTTCT
GGAGTCTGCGACTTCTGAGGCCAGGAGCTTGCCTTTCTGCTGAGTCCAGATTGGCAGATGGACTACCAGTCATACACATG
GCAAAAACCCGCTCCTGGCAGCGGGGAG

Alignment

ORF - retro_mmul_1905 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.57 %
• Parental protein coverage: 57.21 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LADITVVCTLLWLYKQVLEPSFRQAFPNTN-RWFLTCINQPQFRAVLGEVKLCEKMAQFDAKKFAETQPK
          LADI.VVCTL.WLYKQVLEPSF.QAFPNTN..WFL..INQPQFR.VL..VKL.E.MAQFDAKK.AE.Q..
Retrocopy LADIAVVCTLMWLYKQVLEPSFCQAFPNTN<HWFLNFINQPQFRTVLWKVKLSENMAQFDAKKLAESQSE

Parental  KDTPRKEKGSREEKQKPQAERKEEKKAAAPAPEEEMDECEQALAAEPKAKDPFAHLPKSTFVLDEFKRKY
          KD.P.K.KGSRE.KQ..QAERKEEKKAAAPAPEEEMDE.EQ.LAAEPK.KD.FAH...STFVLDEFK.KY
Retrocopy KDIPWKGKGSRERKQ*LQAERKEEKKAAAPAPEEEMDEREQVLAAEPKVKDFFAHFLRSTFVLDEFKHKY

Parental  SNEDTLSVALPYFWEHFDKDGWSLWYSEYRFPEELTQTFMSCNLITGMFQRLDKLRK-NAFASVILFGTN
          SNEDT..V.LPYFWEHFDKD.WSLW.SEY.FP.ELTQTFM.CNLITGMF.RLDKLRK..AFASVILFGT.
Retrocopy SNEDTHFVVLPYFWEHFDKDDWSLW*SEYLFPKELTQTFMTCNLITGMFKRLDKLRK<DAFASVILFGTD

Parental  NSSSISGVWVFRGQELAFPLSPDWQVDYESYTWRKLDPGSEE
          ..SSISGV..F.GQELAF.LSPDWQ.DY.SYTW.K..PGS.E
Retrocopy KGSSISGVCDF*GQELAFLLSPDWQMDYQSYTWQKPAPGSGE

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	0.00 RPM	42.58 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	146.36 RPM
SRP007412_cerebellum	0.00 RPM	48.17 RPM
SRP007412_heart	0.00 RPM	190.08 RPM
SRP007412_kidney	0.00 RPM	97.65 RPM
SRP007412_liver	0.00 RPM	117.09 RPM
SRP007412_testis	0.00 RPM	435.70 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1905 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1905 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1905 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2982
Pan troglodytes	retro_ptro_2017
Gorilla gorilla	retro_ggor_2065

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 53 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015834	6 retrocopies	retro_cfam_1241, retro_cfam_1398, retro_cfam_1862, retro_cfam_478, retro_cfam_638, retro_cfam_653,
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,
Gorilla gorilla	ENSGGOG00000013557	12 retrocopies	retro_ggor_1935, retro_ggor_1936, retro_ggor_1991, retro_ggor_1992, retro_ggor_2064, retro_ggor_2065, retro_ggor_2214, retro_ggor_243, retro_ggor_2542, retro_ggor_2633, retro_ggor_2946, retro_ggor_2947,
Latimeria chalumnae	ENSLACG00000014700	1 retrocopy	retro_lcha_82,
Loxodonta africana	ENSLAFG00000003339	1 retrocopy	retro_lafr_381,
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,
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,
Pan troglodytes	ENSPTRG00000003768	3 retrocopies	retro_ptro_1879, retro_ptro_2017, retro_ptro_3159,
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,
Ictidomys tridecemlineatus	ENSSTOG00000002851	2 retrocopies	retro_itri_852, retro_itri_886,