RetrogeneDB ID: retro_lcha_12

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: JH128015.1:119119..119569(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLACG00000004342
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSLACG00000016164
• Aliases: None
• Description: None

Sequence

>retro_lcha_12
GCACTTCCCTTCATGCCACGGACAGAAATGGCTCCTTATAAGGGTAAAGAAAAGAAGGAAGAACAGGTGATCAGCCTGAG
TCCTCAGGATGCAAAGGGAAAAAATATTTTTGGAGTCTGCCACATCTTTACTTCCTTCAACGACACTCTTGTCCATCTTA
CAGATCAGTCTGGCAAGGAAACTATCTGCTGTATGACCAGCAGTATGAAGGTGAAGGCCAACACGGATGAGTCCTCCCCC
TATGCTGCCACGCTAGCTGCTCAGGATGTTGCCCAGAGGTGCAAGGAGCTGGGCATCACTGCTTTCTACATGAAGCTGCA
TGCTACTTGGGGAAACAGAACCAAGATCCCTGGATTCTGTGCACAGTCTGCCCTCAGAGCTCTGGTCTGTTTTGGCATGA
AAATTGGGCATATTGAGGATATCATTTCCATTCCATCTGACAGCACTTGA

Alignment

ORF - retro_lcha_12 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.46 %
• Parental protein coverage: 87.12 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TEMAPRKGKEKKEEQVISLGPQVAEGENVFGVCHIFASFNDTFVHVTDLSGKETICRVTGGMKVKADRDE
          TEMAP.KGKEKKEEQVISL.PQ.A.G.N.FGVCHIF.SFNDT.VH.TD.SGKETIC..T..MKVKA..DE
Retrocopy TEMAPYKGKEKKEEQVISLSPQDAKGKNIFGVCHIFTSFNDTLVHLTDQSGKETICCMTSSMKVKANTDE

Parental  SSPYAAMLAAQDVAQRCKELGITALHIKLRATGGNRTKTPGPGAQSALRALARSGMKIGRIEDVTPIPSD
          SSPYAA.LAAQDVAQRCKELGITA...KL.AT.GNRTK.PG..AQSALRAL...GMKIG.IED...IPSD
Retrocopy SSPYAATLAAQDVAQRCKELGITAFYMKLHATWGNRTKIPGFCAQSALRALVCFGMKIGHIEDIISIPSD

Parental  ST
          ST
Retrocopy ST

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	678.98 RPM
DRP000627_kidney	0.00 RPM	751.04 RPM
DRP000627_pectoral_fin	0.00 RPM	1096.78 RPM
DRP000627_pelvic_fin	0.00 RPM	1296.99 RPM
DRP000627_pharynx	0.00 RPM	371.31 RPM
DRP000627_tail_muscle	0.00 RPM	261.93 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_12 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 34 parental genes, and 130 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000015004	1 retrocopy	retro_acar_201,
Ailuropoda melanoleuca	ENSAMEG00000004644	2 retrocopies	retro_amel_1390, retro_amel_524,
Bos taurus	ENSBTAG00000008570	2 retrocopies	retro_btau_1109, retro_btau_213,
Canis familiaris	ENSCAFG00000018094	2 retrocopies	retro_cfam_1589, retro_cfam_301,
Callithrix jacchus	ENSCJAG00000020981	1 retrocopy	retro_cjac_89,
Cavia porcellus	ENSCPOG00000024408	2 retrocopies	retro_cpor_253, retro_cpor_284,
Dipodomys ordii	ENSDORG00000007146	2 retrocopies	retro_dord_174, retro_dord_330,
Equus caballus	ENSECAG00000024336	3 retrocopies	retro_ecab_127, retro_ecab_282, retro_ecab_522,
Erinaceus europaeus	ENSEEUG00000010462	3 retrocopies	retro_eeur_330, retro_eeur_423, retro_eeur_617,
Echinops telfairi	ENSETEG00000002899	6 retrocopies	retro_etel_1270, retro_etel_1358, retro_etel_1851, retro_etel_1995, retro_etel_293, retro_etel_967,
Felis catus	ENSFCAG00000011085	5 retrocopies	retro_fcat_1140, retro_fcat_622, retro_fcat_670, retro_fcat_857, retro_fcat_925,
Homo sapiens	ENSG00000164587	8 retrocopies	retro_hsap_119, retro_hsap_1622, retro_hsap_268, retro_hsap_3001, retro_hsap_3113, retro_hsap_3232, retro_hsap_3495, retro_hsap_3789,
Gorilla gorilla	ENSGGOG00000024593	8 retrocopies	retro_ggor_1225, retro_ggor_2080, retro_ggor_2135, retro_ggor_2199, retro_ggor_222, retro_ggor_2362, retro_ggor_2548, retro_ggor_316,
Latimeria chalumnae	ENSLACG00000016164	1 retrocopy	retro_lcha_12 ,
Loxodonta africana	ENSLAFG00000031195	2 retrocopies	retro_lafr_235, retro_lafr_67,
Macropus eugenii	ENSMEUG00000014907	1 retrocopy	retro_meug_619,
Microcebus murinus	ENSMICG00000002900	2 retrocopies	retro_mmur_1569, retro_mmur_433,
Myotis lucifugus	ENSMLUG00000013279	4 retrocopies	retro_mluc_1837, retro_mluc_205, retro_mluc_2464, retro_mluc_2485,
Macaca mulatta	ENSMMUG00000002848	5 retrocopies	retro_mmul_1921, retro_mmul_1983, retro_mmul_358, retro_mmul_570, retro_mmul_90,
Mustela putorius furo	ENSMPUG00000013776	1 retrocopy	retro_mputfur_127,
Mus musculus	ENSMUSG00000024608	5 retrocopies	retro_mmus_1362, retro_mmus_1924, retro_mmus_2178, retro_mmus_2252, retro_mmus_2380,
Nomascus leucogenys	ENSNLEG00000010366	1 retrocopy	retro_nleu_101,
Oryctolagus cuniculus	ENSOCUG00000011509	1 retrocopy	retro_ocun_128,
Otolemur garnettii	ENSOGAG00000000721	1 retrocopy	retro_ogar_286,
Ochotona princeps	ENSOPRG00000008422	17 retrocopies	retro_opri_1012, retro_opri_1074, retro_opri_114, retro_opri_194, retro_opri_258, retro_opri_268, retro_opri_28, retro_opri_306, retro_opri_376, retro_opri_428, retro_opri_707, retro_opri_825, retro_opri_842, retro_opri_876, retro_opri_882, retro_opri_919, retro_opri_971,
Procavia capensis	ENSPCAG00000015960	3 retrocopies	retro_pcap_198, retro_pcap_443, retro_pcap_73,
Pongo abelii	ENSPPYG00000015950	7 retrocopies	retro_pabe_1340, retro_pabe_2487, retro_pabe_2571, retro_pabe_2888, retro_pabe_3204, retro_pabe_401, retro_pabe_494,
Pelodiscus sinensis	ENSPSIG00000005922	1 retrocopy	retro_psin_33,
Pan troglodytes	ENSPTRG00000017418	8 retrocopies	retro_ptro_1086, retro_ptro_130, retro_ptro_2030, retro_ptro_2104, retro_ptro_2184, retro_ptro_224, retro_ptro_2367, retro_ptro_2570,
Rattus norvegicus	ENSRNOG00000018774	10 retrocopies	retro_rnor_1313, retro_rnor_1467, retro_rnor_1532, retro_rnor_1759, retro_rnor_1875, retro_rnor_1918, retro_rnor_2181, retro_rnor_228, retro_rnor_2728, retro_rnor_873,
Sorex araneus	ENSSARG00000014249	1 retrocopy	retro_sara_537,
Sarcophilus harrisii	ENSSHAG00000018052	3 retrocopies	retro_shar_380, retro_shar_381, retro_shar_503,
Tupaia belangeri	ENSTBEG00000006368	10 retrocopies	retro_tbel_1147, retro_tbel_1332, retro_tbel_1603, retro_tbel_1868, retro_tbel_202, retro_tbel_3517, retro_tbel_3619, retro_tbel_416, retro_tbel_519, retro_tbel_740,
Tursiops truncatus	ENSTTRG00000013035	1 retrocopy	retro_ttru_566,