RetrogeneDB ID: retro_lcha_124

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: JH130455.1:108293..108464(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: rps21 (1 of 2)
• Ensembl ID: ENSLACG00000012753
• Aliases: None
• Description: ribosomal protein S21 [Source:ZFIN;Acc:ZDB-GENE-040426-1102]

Sequence

>retro_lcha_124
ATGCAAAATGACACTTGGTAATTATCTGGATCTATATGTCCCGCATAATTGCTCCACTAGCAACAGAATTGTTGATTTCA
AGGATCACATTTCCGTTCAGCTGAATCTTGCCGAGGTTGACAAGCGCACAGGCAGGTTAATTGGATATAAGACCTTGTTA
TCTGTGGAGCC

Alignment

ORF - retro_lcha_124 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.33 %
• Parental protein coverage: 69.88 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MQNDA-GEFVDLYVPRKCSASNRIIGAKDHASIQLNLAEVDRLTGRFNGQFKT-YAICGA
          MQND..G...DLYVP..CS.SNRI...KDH.S.QLNLAEVD..TGR..G..KT...ICGA
Retrocopy MQNDT>GNYLDLYVPHNCSTSNRIVDFKDHISVQLNLAEVDKRTGRLIG-YKT<LVICGA

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	314.62 RPM
DRP000627_kidney	0.00 RPM	459.90 RPM
DRP000627_pectoral_fin	0.00 RPM	593.06 RPM
DRP000627_pelvic_fin	0.00 RPM	478.90 RPM
DRP000627_pharynx	0.00 RPM	186.07 RPM
DRP000627_tail_muscle	0.00 RPM	121.75 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_124 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 112 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017399	2 retrocopies	retro_amel_1783, retro_amel_87,
Bos taurus	ENSBTAG00000020795	2 retrocopies	retro_btau_174, retro_btau_1780,
Canis familiaris	ENSCAFG00000012676	4 retrocopies	retro_cfam_1055, retro_cfam_1687, retro_cfam_1896, retro_cfam_28,
Callithrix jacchus	ENSCJAG00000014195	5 retrocopies	retro_cjac_2266, retro_cjac_2572, retro_cjac_629, retro_cjac_82, retro_cjac_884,
Cavia porcellus	ENSCPOG00000001965	4 retrocopies	retro_cpor_1156, retro_cpor_1268, retro_cpor_262, retro_cpor_584,
Erinaceus europaeus	ENSEEUG00000004573	2 retrocopies	retro_eeur_235, retro_eeur_501,
Homo sapiens	ENSG00000171858	6 retrocopies	retro_hsap_1179, retro_hsap_1883, retro_hsap_2300, retro_hsap_2949, retro_hsap_3026, retro_hsap_4303,
Gorilla gorilla	ENSGGOG00000023745	7 retrocopies	retro_ggor_131, retro_ggor_1380, retro_ggor_1647, retro_ggor_2043, retro_ggor_2089, retro_ggor_2875, retro_ggor_917,
Latimeria chalumnae	ENSLACG00000012753	1 retrocopy	retro_lcha_124 ,
Loxodonta africana	ENSLAFG00000015793	4 retrocopies	retro_lafr_1055, retro_lafr_1237, retro_lafr_352, retro_lafr_499,
Macropus eugenii	ENSMEUG00000015832	2 retrocopies	retro_meug_1221, retro_meug_466,
Microcebus murinus	ENSMICG00000012997	5 retrocopies	retro_mmur_110, retro_mmur_1388, retro_mmur_264, retro_mmur_55, retro_mmur_965,
Myotis lucifugus	ENSMLUG00000000346	3 retrocopies	retro_mluc_1009, retro_mluc_2136, retro_mluc_2282,
Macaca mulatta	ENSMMUG00000005006	8 retrocopies	retro_mmul_1006, retro_mmul_1043, retro_mmul_1138, retro_mmul_1279, retro_mmul_1331, retro_mmul_1948, retro_mmul_588, retro_mmul_633,
Monodelphis domestica	ENSMODG00000016769	1 retrocopy	retro_mdom_464,
Mus musculus	ENSMUSG00000039001	11 retrocopies	retro_mmus_1100, retro_mmus_1324, retro_mmus_1482, retro_mmus_1510, retro_mmus_1688, retro_mmus_1837, retro_mmus_2039, retro_mmus_2071, retro_mmus_2243, retro_mmus_576, retro_mmus_992,
Ornithorhynchus anatinus	ENSOANG00000003361	2 retrocopies	retro_oana_102, retro_oana_107,
Otolemur garnettii	ENSOGAG00000016673	12 retrocopies	retro_ogar_1013, retro_ogar_1339, retro_ogar_1742, retro_ogar_2111, retro_ogar_2176, retro_ogar_2532, retro_ogar_2703, retro_ogar_2921, retro_ogar_3119, retro_ogar_3214, retro_ogar_3256, retro_ogar_719,
Ochotona princeps	ENSOPRG00000000937	1 retrocopy	retro_opri_996,
Pongo abelii	ENSPPYG00000011205	8 retrocopies	retro_pabe_1562, retro_pabe_157, retro_pabe_2446, retro_pabe_2505, retro_pabe_3503, retro_pabe_365, retro_pabe_710, retro_pabe_986,
Pan troglodytes	ENSPTRG00000013708	1 retrocopy	retro_ptro_42,
Pteropus vampyrus	ENSPVAG00000003548	2 retrocopies	retro_pvam_1362, retro_pvam_1368,
Rattus norvegicus	ENSRNOG00000006325	2 retrocopies	retro_rnor_128, retro_rnor_172,
Sus scrofa	ENSSSCG00000021825	1 retrocopy	retro_sscr_7,
Ictidomys tridecemlineatus	ENSSTOG00000001029	5 retrocopies	retro_itri_1027, retro_itri_1487, retro_itri_637, retro_itri_82, retro_itri_849,
Tarsius syrichta	ENSTSYG00000007061	5 retrocopies	retro_tsyr_105, retro_tsyr_123, retro_tsyr_1502, retro_tsyr_2157, retro_tsyr_951,
Tursiops truncatus	ENSTTRG00000011105	6 retrocopies	retro_ttru_1058, retro_ttru_1418, retro_ttru_1707, retro_ttru_1749, retro_ttru_1773, retro_ttru_674,