RetrogeneDB ID: retro_lcha_2

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: JH127735.1:445932..446388(-)
• Located in intron of: ENSLACG00000009068

Retrocopy information

• Ensembl ID: ENSLACG00000009755
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: rps13 (1 of 3)
• Ensembl ID: ENSLACG00000017174
• Aliases: None
• Description: ribosomal protein S13 [Source:ZFIN;Acc:ZDB-GENE-040625-52]

Sequence

>retro_lcha_2
ATGGGTCGTATGCACGCTCCGGGAAAGGGCTTGTCCCAATCAGCTCTGCCTTACAGACGTAGTGTGCCCACATGGCTGAA
ACTTACGTCTGATGATGTGAAGGAACAGATCTTTAAACTGGCCAAGAAAGGTCTGACACCTTCACAGATTGGTGTTATCC
TGAGGGACTCCCATGGTGTTGCCCAAGTGCGTTTTGTTACTGGCAACAAAATCCTGAGAATCCTTAAGTCTAAGGGTTTG
GCTCCAGATCTTCCAGAGGATCTGTATCATCTCATCAAGAAGGCTGTTGCTGTCCGCAAACACCTTGAGAGGAACAGAAA
GGATAAGGATGCCAAGTTCCGTCTGATTTTGATTGAAAGCAGAATCCACAGGCTGGCTCGTTATTACAAGACCAAGAGAG
TACTTCCTCCCAATTGGAAATATGAATCATCCACAGCTTCAGCTCTTGTTGCCTAA

Alignment

ORF - retro_lcha_2 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100. %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGRMHAPGKGLSQSALPYRRSVPTWLKLTSDDVKEQIFKLAKKGLTPSQIGVILRDSHGVAQVRFVTGNK
          MGRMHAPGKGLSQSALPYRRSVPTWLKLTSDDVKEQIFKLAKKGLTPSQIGVILRDSHGVAQVRFVTGNK
Retrocopy MGRMHAPGKGLSQSALPYRRSVPTWLKLTSDDVKEQIFKLAKKGLTPSQIGVILRDSHGVAQVRFVTGNK

Parental  ILRILKSKGLAPDLPEDLYHLIKKAVAVRKHLERNRKDKDAKFRLILIESRIHRLARYYKTKRVLPPNWK
          ILRILKSKGLAPDLPEDLYHLIKKAVAVRKHLERNRKDKDAKFRLILIESRIHRLARYYKTKRVLPPNWK
Retrocopy ILRILKSKGLAPDLPEDLYHLIKKAVAVRKHLERNRKDKDAKFRLILIESRIHRLARYYKTKRVLPPNWK

Parental  YESSTASALVA
          YESSTASALVA
Retrocopy YESSTASALVA

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	24.64 RPM	358.99 RPM
DRP000627_kidney	28.19 RPM	376.34 RPM
DRP000627_pectoral_fin	42.94 RPM	475.90 RPM
DRP000627_pelvic_fin	24.35 RPM	529.74 RPM
DRP000627_pharynx	16.88 RPM	261.19 RPM
DRP000627_tail_muscle	13.77 RPM	166.85 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_2 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 35 parental genes, and 161 retrocopies.

Species	Parental gene accession	Retrocopies number
Caenorhabditis elegans	C16A3.9	1 retrocopy	retro_cele_6,
Ailuropoda melanoleuca	ENSAMEG00000002895	3 retrocopies	retro_amel_1451, retro_amel_1788, retro_amel_694,
Bos taurus	ENSBTAG00000040308	5 retrocopies	retro_btau_1286, retro_btau_266, retro_btau_284, retro_btau_46, retro_btau_784,
Choloepus hoffmanni	ENSCHOG00000008721	4 retrocopies	retro_chof_1484, retro_chof_1497, retro_chof_1644, retro_chof_2359,
Callithrix jacchus	ENSCJAG00000009564	1 retrocopy	retro_cjac_356,
Cavia porcellus	ENSCPOG00000000023	3 retrocopies	retro_cpor_1535, retro_cpor_400, retro_cpor_526,
Dipodomys ordii	ENSDORG00000002507	3 retrocopies	retro_dord_397, retro_dord_57, retro_dord_759,
Equus caballus	ENSECAG00000014928	12 retrocopies	retro_ecab_1037, retro_ecab_1047, retro_ecab_1065, retro_ecab_1066, retro_ecab_170, retro_ecab_304, retro_ecab_696, retro_ecab_777, retro_ecab_804, retro_ecab_822, retro_ecab_891, retro_ecab_954,
Felis catus	ENSFCAG00000005370	2 retrocopies	retro_fcat_407, retro_fcat_598,
Homo sapiens	ENSG00000110700	6 retrocopies	retro_hsap_1499, retro_hsap_1574, retro_hsap_2098, retro_hsap_251, retro_hsap_3242, retro_hsap_388,
Gorilla gorilla	ENSGGOG00000007450	3 retrocopies	retro_ggor_127, retro_ggor_2207, retro_ggor_303,
Latimeria chalumnae	ENSLACG00000017174	1 retrocopy	retro_lcha_2 ,
Loxodonta africana	ENSLAFG00000026881	3 retrocopies	retro_lafr_1179, retro_lafr_382, retro_lafr_511,
Macropus eugenii	ENSMEUG00000014986	2 retrocopies	retro_meug_635, retro_meug_797,
Microcebus murinus	ENSMICG00000003716	8 retrocopies	retro_mmur_1109, retro_mmur_1620, retro_mmur_172, retro_mmur_460, retro_mmur_588, retro_mmur_85, retro_mmur_880, retro_mmur_904,
Myotis lucifugus	ENSMLUG00000009751	3 retrocopies	retro_mluc_174, retro_mluc_2470, retro_mluc_899,
Macaca mulatta	ENSMMUG00000022547	2 retrocopies	retro_mmul_330, retro_mmul_40,
Monodelphis domestica	ENSMODG00000007078	6 retrocopies	retro_mdom_1108, retro_mdom_1150, retro_mdom_1895, retro_mdom_1965, retro_mdom_566, retro_mdom_599,
Mustela putorius furo	ENSMPUG00000013316	1 retrocopy	retro_mputfur_181,
Mus musculus	ENSMUSG00000090862	19 retrocopies	retro_mmus_1062, retro_mmus_1124, retro_mmus_1526, retro_mmus_1563, retro_mmus_1980, retro_mmus_2210, retro_mmus_2642, retro_mmus_2830, retro_mmus_2831, retro_mmus_2832, retro_mmus_2906, retro_mmus_3050, retro_mmus_3092, retro_mmus_3153, retro_mmus_3236, retro_mmus_328, retro_mmus_3423, retro_mmus_775, retro_mmus_807,
Nomascus leucogenys	ENSNLEG00000026739	4 retrocopies	retro_nleu_1304, retro_nleu_1693, retro_nleu_2439, retro_nleu_858,
Ornithorhynchus anatinus	ENSOANG00000007687	1 retrocopy	retro_oana_98,
Oryctolagus cuniculus	ENSOCUG00000005536	6 retrocopies	retro_ocun_1337, retro_ocun_1523, retro_ocun_1929, retro_ocun_673, retro_ocun_740, retro_ocun_909,
Otolemur garnettii	ENSOGAG00000002128	7 retrocopies	retro_ogar_1567, retro_ogar_1595, retro_ogar_1818, retro_ogar_2751, retro_ogar_3441, retro_ogar_502, retro_ogar_844,
Ochotona princeps	ENSOPRG00000000162	5 retrocopies	retro_opri_1107, retro_opri_239, retro_opri_390, retro_opri_487, retro_opri_57,
Pongo abelii	ENSPPYG00000003456	6 retrocopies	retro_pabe_1250, retro_pabe_1298, retro_pabe_2001, retro_pabe_2012, retro_pabe_2689, retro_pabe_408,
Pteropus vampyrus	ENSPVAG00000012806	3 retrocopies	retro_pvam_1143, retro_pvam_698, retro_pvam_880,
Rattus norvegicus	ENSRNOG00000020502	2 retrocopies	retro_rnor_190, retro_rnor_377,
Sarcophilus harrisii	ENSSHAG00000004052	3 retrocopies	retro_shar_183, retro_shar_298, retro_shar_589,
Sus scrofa	ENSSSCG00000013381	5 retrocopies	retro_sscr_1209, retro_sscr_264, retro_sscr_333, retro_sscr_711, retro_sscr_738,
Ictidomys tridecemlineatus	ENSSTOG00000008996	5 retrocopies	retro_itri_1011, retro_itri_1905, retro_itri_329, retro_itri_493, retro_itri_881,
Tupaia belangeri	ENSTBEG00000007717	7 retrocopies	retro_tbel_1777, retro_tbel_2022, retro_tbel_3850, retro_tbel_3913, retro_tbel_4204, retro_tbel_661, retro_tbel_902,
Tarsius syrichta	ENSTSYG00000013114	11 retrocopies	retro_tsyr_133, retro_tsyr_1352, retro_tsyr_1447, retro_tsyr_1460, retro_tsyr_1712, retro_tsyr_1900, retro_tsyr_1967, retro_tsyr_247, retro_tsyr_51, retro_tsyr_887, retro_tsyr_904,
Tursiops truncatus	ENSTTRG00000016321	3 retrocopies	retro_ttru_1168, retro_ttru_1435, retro_ttru_737,
Vicugna pacos	ENSVPAG00000001463	5 retrocopies	retro_vpac_117, retro_vpac_247, retro_vpac_415, retro_vpac_473, retro_vpac_525,