RetrogeneDB ID: retro_lcha_57

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: JH127029.1:254714..254995(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSLACG00000008511
• Aliases: None
• Description: None

Sequence

>retro_lcha_57
GGCATTATGGTGGAGCGATTCGTAGGAACGTGAAAAACAAGCCCAGTGAGAATTCTGATGATTAAATGAAAGTGTTGGGG
GTGGGTTTTGCCACCGGAACACTTGGTAGTGTAACCAAACTGGATGTGGTTGTGTCTGTAGACAGGGATTAGAGCACCAT
AAATATGGAAAGTACCGTGAAAACCACCTCGGTCGCGTTTAAACTGGGAGAGGAATTTGATGAAACTGCAGCAGACAACA
GGAAAACGAAGGCTGTCATTAATCTGGAAAATGGTAAGCTT

Alignment

ORF - retro_lcha_57 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.74 %
• Parental protein coverage: 70.15 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GIMVDQFVGTWKL-ETSDNFDDYMKALGVGFATRTLGSVTKPSVVVSVDGDRITIKTESTVKTTSVTFKL
          GIMV..FVGT.K....S.N.DD.MK.LGVGFAT.TLGSVTK..VVVSVD.D..TI..ESTVKTTSV.FKL
Retrocopy GIMVERFVGT*KT<KPSENSDD*MKVLGVGFATGTLGSVTKLDVVVSVDRD*STINMESTVKTTSVAFKL

Parental  GEEFDETTADDRKTKTVFNLENGKL
          GEEFDET.AD.RKTK.V.NLENGKL
Retrocopy GEEFDETAADNRKTKAVINLENGKL

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	0.00 RPM	0.12 RPM
DRP000627_kidney	0.00 RPM	0.04 RPM
DRP000627_pectoral_fin	0.00 RPM	0.06 RPM
DRP000627_pelvic_fin	0.00 RPM	0.11 RPM
DRP000627_pharynx	0.00 RPM	0.06 RPM
DRP000627_tail_muscle	0.00 RPM	0.02 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_57 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 42 parental genes, and 130 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000013564	1 retrocopy	retro_acar_190,
Ailuropoda melanoleuca	ENSAMEG00000014554	1 retrocopy	retro_amel_945,
Ailuropoda melanoleuca	ENSAMEG00000014619	1 retrocopy	retro_amel_1139,
Bos taurus	ENSBTAG00000047330	3 retrocopies	retro_btau_1312, retro_btau_1828, retro_btau_886,
Canis familiaris	ENSCAFG00000025410	3 retrocopies	retro_cfam_132, retro_cfam_137, retro_cfam_228,
Callithrix jacchus	ENSCJAG00000000433	1 retrocopy	retro_cjac_2486,
Callithrix jacchus	ENSCJAG00000000444	4 retrocopies	retro_cjac_1832, retro_cjac_2227, retro_cjac_2816, retro_cjac_4084,
Cavia porcellus	ENSCPOG00000025732	1 retrocopy	retro_cpor_948,
Dasypus novemcinctus	ENSDNOG00000018066	5 retrocopies	retro_dnov_1073, retro_dnov_1231, retro_dnov_1318, retro_dnov_2392, retro_dnov_559,
Equus caballus	ENSECAG00000008270	2 retrocopies	retro_ecab_894, retro_ecab_938,
Equus caballus	ENSECAG00000023552	1 retrocopy	retro_ecab_761,
Erinaceus europaeus	ENSEEUG00000014023	2 retrocopies	retro_eeur_405, retro_eeur_627,
Echinops telfairi	ENSETEG00000007443	14 retrocopies	retro_etel_1024, retro_etel_1241, retro_etel_1276, retro_etel_1405, retro_etel_1467, retro_etel_1706, retro_etel_1842, retro_etel_1904, retro_etel_2003, retro_etel_512, retro_etel_602, retro_etel_620, retro_etel_806, retro_etel_994,
Felis catus	ENSFCAG00000006032	2 retrocopies	retro_fcat_1243, retro_fcat_1834,
Homo sapiens	ENSG00000164687	12 retrocopies	retro_hsap_1205, retro_hsap_1279, retro_hsap_1520, retro_hsap_1521, retro_hsap_2167, retro_hsap_2568, retro_hsap_3000, retro_hsap_3357, retro_hsap_3376, retro_hsap_3811, retro_hsap_4717, retro_hsap_880,
Homo sapiens	ENSG00000197416	1 retrocopy	retro_hsap_3679,
Gorilla gorilla	ENSGGOG00000005964	8 retrocopies	retro_ggor_1005, retro_ggor_1163, retro_ggor_2079, retro_ggor_2276, retro_ggor_2284, retro_ggor_2563, retro_ggor_2931, retro_ggor_940,
Gorilla gorilla	ENSGGOG00000016835	1 retrocopy	retro_ggor_2488,
Latimeria chalumnae	ENSLACG00000008511	3 retrocopies	retro_lcha_37, retro_lcha_45, retro_lcha_57 ,
Macropus eugenii	ENSMEUG00000002136	1 retrocopy	retro_meug_1874,
Microcebus murinus	ENSMICG00000001311	2 retrocopies	retro_mmur_137, retro_mmur_702,
Microcebus murinus	ENSMICG00000005319	1 retrocopy	retro_mmur_1131,
Myotis lucifugus	ENSMLUG00000009514	3 retrocopies	retro_mluc_1590, retro_mluc_1920, retro_mluc_501,
Myotis lucifugus	ENSMLUG00000009529	1 retrocopy	retro_mluc_1953,
Macaca mulatta	ENSMMUG00000000486	4 retrocopies	retro_mmul_1417, retro_mmul_1920, retro_mmul_2095, retro_mmul_2230,
Macaca mulatta	ENSMMUG00000010906	1 retrocopy	retro_mmul_1311,
Macaca mulatta	ENSMMUG00000019337	1 retrocopy	retro_mmul_1787,
Mus musculus	ENSMUSG00000027533	4 retrocopies	retro_mmus_1685, retro_mmus_1791, retro_mmus_2084, retro_mmus_3185,
Nomascus leucogenys	ENSNLEG00000002515	1 retrocopy	retro_nleu_528,
Otolemur garnettii	ENSOGAG00000002413	10 retrocopies	retro_ogar_1024, retro_ogar_1151, retro_ogar_1286, retro_ogar_1676, retro_ogar_2873, retro_ogar_3066, retro_ogar_3099, retro_ogar_3265, retro_ogar_715, retro_ogar_878,
Otolemur garnettii	ENSOGAG00000012166	1 retrocopy	retro_ogar_843,
Oryzias latipes	ENSORLG00000008282	1 retrocopy	retro_olat_7,
Pongo abelii	ENSPPYG00000018699	1 retrocopy	retro_pabe_27,
Pongo abelii	ENSPPYG00000018703	1 retrocopy	retro_pabe_3016,
Pan troglodytes	ENSPTRG00000020373	12 retrocopies	retro_ptro_1029, retro_ptro_1030, retro_ptro_1498, retro_ptro_1654, retro_ptro_2029, retro_ptro_2131, retro_ptro_2265, retro_ptro_2295, retro_ptro_2664, retro_ptro_3135, retro_ptro_823, retro_ptro_875,
Pan troglodytes	ENSPTRG00000022654	1 retrocopy	retro_ptro_2493,
Pteropus vampyrus	ENSPVAG00000017850	5 retrocopies	retro_pvam_1159, retro_pvam_467, retro_pvam_531, retro_pvam_852, retro_pvam_89,
Rattus norvegicus	ENSRNOG00000049075	3 retrocopies	retro_rnor_1762, retro_rnor_1879, retro_rnor_1997,
Sus scrofa	ENSSSCG00000006153	1 retrocopy	retro_sscr_476,
Ictidomys tridecemlineatus	ENSSTOG00000007877	3 retrocopies	retro_itri_1305, retro_itri_389, retro_itri_72,
Tarsius syrichta	ENSTSYG00000001472	5 retrocopies	retro_tsyr_126, retro_tsyr_1534, retro_tsyr_1894, retro_tsyr_1982, retro_tsyr_2024,
Tursiops truncatus	ENSTTRG00000005377	1 retrocopy	retro_ttru_1800,