RetrogeneDB ID: retro_lcha_82

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: JH127416.1:106400..107078(+)
• Located in intron of: ENSLACG00000002246

Retrocopy information

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

Parental gene information

• Parental gene symbol: EEF1G
• Ensembl ID: ENSLACG00000014700
• Aliases: None
• Description: eukaryotic translation elongation factor 1 gamma [Source:HGNC Symbol;Acc:3213]

Sequence

>retro_lcha_82
GGGACTCTCTACACTTACCCTGAAAACTGGAGGGCGTTCAAGGCCCTGATCGCTGCGCAGTACAGCGGCGCCACAGTCAA
GGTTCAGTCCACCCCTCCGCAGTTCCATTTCAGGTAGAGCAACAAGACCCCGGAATTCCTCCAGAAGTTCCCACTTGGCA
AGGTTCCTGCCTTTGAGGGAGACGATGGATTCTGCGTGTTCGAGAGCAACGCCATTGCTCATTATGTGAGTAACGATGAA
CTGCGCGGCTCCAGCAAGGTTGCAGCGACTCAGGTTATCCAGTGGATGAGCTTTGCGGACAGTGAGATCGTCCCCCCTGC
CAGCACCTGGGTCTTCCCCACCCTTGGCATCATGCAGTACAACAAGCAGGCGACGGAGCACGCCAAGGAGGAAGTGAAGA
AGGTCCTGGGTGTTCTGGATTTGCACCTGCAGACTCGCACCTTCCTGGTGGGAGAGCGTGTCACCCTAGCGGATATCGCA
GTTGTCTGCTCGCTGCTGTGGCTCTACAAACAGGTTCCAGAACCTTCCTTCCGTCAGCCGTACGTCAATGCTAATTGGTG
GTTTGTGACCTGTGTGAACCAGCCCCAGTTTAAGGCTGTCCTCGGGGAGGTGAAACTCTGTGAGAAAATGGCCCAATTTG
ATGCCAAGAAGGTTGCAGAACCGCAGCCCAAGAAGGAG

Alignment

ORF - retro_lcha_82 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.02 %
• Parental protein coverage: 51.6 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GTLYTYPENWRAFKALIAAQYSGATVKVQSTPPQFHFGQSNKTPEFLQKFPLGKVPAFEGDDGFCVFESN
          GTLYTYPENWRAFKALIAAQYSGATVKVQSTPPQFHF..SNKTPEFLQKFPLGKVPAFEGDDGFCVFESN
Retrocopy GTLYTYPENWRAFKALIAAQYSGATVKVQSTPPQFHFR*SNKTPEFLQKFPLGKVPAFEGDDGFCVFESN

Parental  AIAHYVSNDELRGSSKVAAAQVIQWMSFADSEIVPPASTWVFPTLGIMQYNKQATEHAKEEVKKVLGVLD
          AIAHYVSNDELRGSSKVAA.QVIQWMSFADSEIVPPASTWVFPTLGIMQYNKQATEHAKEEVKKVLGVLD
Retrocopy AIAHYVSNDELRGSSKVAATQVIQWMSFADSEIVPPASTWVFPTLGIMQYNKQATEHAKEEVKKVLGVLD

Parental  LHLQTRTFLVGERVTLADIAVVCSLLWLYKQVLEPSFRQLYVNVNRWFVTCVNQPQFKAVLGEVKLCEKM
          LHLQTRTFLVGERVTLADIAVVCSLLWLYKQV.EPSFRQ.YVN.N.WFVTCVNQPQFKAVLGEVKLCEKM
Retrocopy LHLQTRTFLVGERVTLADIAVVCSLLWLYKQVPEPSFRQPYVNANWWFVTCVNQPQFKAVLGEVKLCEKM

Parental  AQFDAKKFAELQPKKE
          AQFDAKK.AE.QPKKE
Retrocopy AQFDAKKVAEPQPKKE

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
DRP000627_gill	3.51 RPM	836.16 RPM
DRP000627_kidney	4.84 RPM	925.38 RPM
DRP000627_pectoral_fin	5.04 RPM	926.43 RPM
DRP000627_pelvic_fin	7.19 RPM	1090.04 RPM
DRP000627_pharynx	3.22 RPM	857.86 RPM
DRP000627_tail_muscle	2.54 RPM	656.52 RPM

ChIP-Seq

Latimeria chalumnae was not studied using ChIP-Seq data.

EST

Latimeria chalumnae was not studied using EST data.

TSS

Latimeria chalumnae was not studied using FANTOM5 data.

Lab

retro_lcha_82 was not experimentally validated.

Homology

Retrocopy orthology:

Latimeria chalumnae does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 27 parental genes, and 81 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,
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,
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,