RetrogeneDB ID: retro_lcha_26

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: JH126590.1:368980..369461(-)
• Located in intron of: ENSLACG00000007956

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS10
• Ensembl ID: ENSLACG00000017219
• Aliases: None
• Description: None

Sequence

>retro_lcha_26
GGTGAAGCCACAGAGATGCTGATGCCCCCAAAAGAATCATATTGCCATCTGCAAGCTCCTCTTCAAGGAAGGAATGATGA
TGGCCGAGAAGGATGGTCGCAAACCCAAACAACCTGAACTAGCAGACAGGAATGTGCCTAACCTCTATGTCATGAAGGCC
ATGCGGTCTCTGAAATCTCCTGGCTTTCTGAAGGAACAGTTTGCCTGGTGTTGCTTTTACTGGTATCTAACCAACTAAAG
GTATCCAGTACCTCCATGGATTTCCTTCACCTGCCACCTGAAACTGTTCCCACTACCCTGCATCACCAGACCTGCCCTGA
CACTGCCAGGCCCAAACCTAAAGATTTGGAAGAAAAGCGCCCTGTTCGTCTGGCCTGTGGCGATACTGACAGAGATACAT
ACAGACGCAATGCTGCTCCCACCTGGTGCTGACAAAAAGGCCGAGTCTGTTGCAGCTACAGAATTCCAGTTTAGGGGAGG
A

Alignment

ORF - retro_lcha_26 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.73 %
• Parental protein coverage: 91.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GLNVEMLMP-KKNRIAIYELLFKEGVMVAKKDVHMPKHPELADRNVPNLHVMKAMQSLKSRGYVKEQFAW
          G...EMLMP..KN.IAI..LLFKEG.M.A.KD...PK.PELADRNVPNL.VMKAM.SLKS.G..KEQFAW
Retrocopy GEATEMLMP>QKNHIAICKLLFKEGMMMAEKDGRKPKQPELADRNVPNLYVMKAMRSLKSPGFLKEQFAW

Parental  RHFYWYLTN-EGIQYLR-DFLHLPPEIVPATLRRQTRPETARPRPKGLEGERPARLARGETDRDTYRRSA
          ..FYWYLTN..GIQYL..DFLHLPPE.VP.TL..QT.P.TARP.PK.LE..RP.RLA.G.TDRDTYRR.A
Retrocopy CCFYWYLTN>KGIQYLH>DFLHLPPETVPTTLHHQTCPDTARPKPKDLEEKRPVRLACGDTDRDTYRRNA

Parental  A-PPGADKKAEAGAGAATEFQFRGG
          A.PPGADKKAE....AATEFQFRGG
Retrocopy A>PPGADKKAE--SVAATEFQFRGG

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	0.01 RPM	570.33 RPM
DRP000627_kidney	0.00 RPM	551.97 RPM
DRP000627_pectoral_fin	0.00 RPM	955.82 RPM
DRP000627_pelvic_fin	0.00 RPM	941.10 RPM
DRP000627_pharynx	0.01 RPM	375.03 RPM
DRP000627_tail_muscle	0.02 RPM	263.04 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_26 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 30 parental genes, and 165 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001047	4 retrocopies	retro_amel_1408, retro_amel_1706, retro_amel_446, retro_amel_890,
Bos taurus	ENSBTAG00000015598	3 retrocopies	retro_btau_1334, retro_btau_844, retro_btau_989,
Canis familiaris	ENSCAFG00000001214	2 retrocopies	retro_cfam_1, retro_cfam_92,
Callithrix jacchus	ENSCJAG00000015250	4 retrocopies	retro_cjac_215, retro_cjac_296, retro_cjac_325, retro_cjac_63,
Cavia porcellus	ENSCPOG00000008613	2 retrocopies	retro_cpor_1245, retro_cpor_345,
Dasypus novemcinctus	ENSDNOG00000011670	2 retrocopies	retro_dnov_2303, retro_dnov_2558,
Dipodomys ordii	ENSDORG00000012060	6 retrocopies	retro_dord_225, retro_dord_494, retro_dord_641, retro_dord_73, retro_dord_74, retro_dord_767,
Equus caballus	ENSECAG00000006430	1 retrocopy	retro_ecab_198,
Erinaceus europaeus	ENSEEUG00000003376	2 retrocopies	retro_eeur_367, retro_eeur_647,
Felis catus	ENSFCAG00000015355	3 retrocopies	retro_fcat_1443, retro_fcat_1681, retro_fcat_1757,
Homo sapiens	ENSG00000124614	24 retrocopies	retro_hsap_1509, retro_hsap_1628, retro_hsap_1630, retro_hsap_1657, retro_hsap_1923, retro_hsap_2003, retro_hsap_2113, retro_hsap_229, retro_hsap_2415, retro_hsap_2573, retro_hsap_2574, retro_hsap_2830, retro_hsap_289, retro_hsap_3007, retro_hsap_3170, retro_hsap_3243, retro_hsap_3436, retro_hsap_3454, retro_hsap_3720, retro_hsap_4114, retro_hsap_4190, retro_hsap_460, retro_hsap_869, retro_hsap_992,
Latimeria chalumnae	ENSLACG00000017219	1 retrocopy	retro_lcha_26 ,
Loxodonta africana	ENSLAFG00000008539	1 retrocopy	retro_lafr_756,
Myotis lucifugus	ENSMLUG00000007495	2 retrocopies	retro_mluc_1143, retro_mluc_2128,
Macaca mulatta	ENSMMUG00000000267	2 retrocopies	retro_mmul_332, retro_mmul_555,
Monodelphis domestica	ENSMODG00000013929	2 retrocopies	retro_mdom_1889, retro_mdom_437,
Mustela putorius furo	ENSMPUG00000003117	3 retrocopies	retro_mputfur_1347, retro_mputfur_1533, retro_mputfur_1579,
Mus musculus	ENSMUSG00000052146	9 retrocopies	retro_mmus_1376, retro_mmus_1500, retro_mmus_1831, retro_mmus_2431, retro_mmus_2551, retro_mmus_2708, retro_mmus_3651, retro_mmus_5, retro_mmus_858,
Nomascus leucogenys	ENSNLEG00000008336	24 retrocopies	retro_nleu_1064, retro_nleu_1206, retro_nleu_1217, retro_nleu_1366, retro_nleu_1463, retro_nleu_1496, retro_nleu_165, retro_nleu_1694, retro_nleu_1748, retro_nleu_1969, retro_nleu_2120, retro_nleu_2452, retro_nleu_2678, retro_nleu_2791, retro_nleu_2833, retro_nleu_2834, retro_nleu_2950, retro_nleu_2955, retro_nleu_3021, retro_nleu_3047, retro_nleu_3052, retro_nleu_579, retro_nleu_850, retro_nleu_882,
Oryctolagus cuniculus	ENSOCUG00000011373	2 retrocopies	retro_ocun_250, retro_ocun_874,
Otolemur garnettii	ENSOGAG00000001365	5 retrocopies	retro_ogar_2166, retro_ogar_2314, retro_ogar_2553, retro_ogar_415, retro_ogar_873,
Ochotona princeps	ENSOPRG00000002693	2 retrocopies	retro_opri_297, retro_opri_800,
Procavia capensis	ENSPCAG00000012795	1 retrocopy	retro_pcap_309,
Pongo abelii	ENSPPYG00000016516	2 retrocopies	retro_pabe_2319, retro_pabe_97,
Pan troglodytes	ENSPTRG00000018063	26 retrocopies	retro_ptro_1021, retro_ptro_1090, retro_ptro_1092, retro_ptro_1126, retro_ptro_1160, retro_ptro_1287, retro_ptro_1335, retro_ptro_1391, retro_ptro_1497, retro_ptro_1502, retro_ptro_1503, retro_ptro_1788, retro_ptro_1918, retro_ptro_199, retro_ptro_2192, retro_ptro_2330, retro_ptro_2342, retro_ptro_238, retro_ptro_2519, retro_ptro_2793, retro_ptro_2797, retro_ptro_2919, retro_ptro_3051, retro_ptro_3078, retro_ptro_347, retro_ptro_603,
Rattus norvegicus	ENSRNOG00000000490	4 retrocopies	retro_rnor_169, retro_rnor_224, retro_rnor_359, retro_rnor_74,
Sarcophilus harrisii	ENSSHAG00000000731	3 retrocopies	retro_shar_243, retro_shar_334, retro_shar_724,
Ictidomys tridecemlineatus	ENSSTOG00000013486	5 retrocopies	retro_itri_1448, retro_itri_1515, retro_itri_230, retro_itri_787, retro_itri_963,
Tupaia belangeri	ENSTBEG00000001492	16 retrocopies	retro_tbel_1302, retro_tbel_175, retro_tbel_1775, retro_tbel_2039, retro_tbel_2061, retro_tbel_2062, retro_tbel_2766, retro_tbel_2814, retro_tbel_314, retro_tbel_3359, retro_tbel_483, retro_tbel_522, retro_tbel_667, retro_tbel_980, retro_tbel_981, retro_tbel_986,
Tursiops truncatus	ENSTTRG00000015064	2 retrocopies	retro_ttru_1089, retro_ttru_1211,