RetrogeneDB ID: retro_lcha_50

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: JH126955.1:838967..839287(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS25
• Ensembl ID: ENSLACG00000017531
• Aliases: None
• Description: None

Sequence

>retro_lcha_50
ATACCTCCCAAGGGCAATAAGAAGGATGCTTGGAAGAGTGCCAAAGACAAGTGCTCAGTAAACAAGTCTAGTGGCAAAGT
TAAGAAAAAAGTTGTCCAGGGCAAAATGTGAGGGACAAGCTGAATAACTTGGTGCTCTCTGAAAAGGCCACTTATAACAA
ACTTTATAGGGAACTGCCCAATTACAAACTCATCACACCCGCCATGGTGAAGAACAAAAGATCTCTAGCCAGTGCTGTCC
TTCAGGAACTGCTCATAGAAGGTATGGTTATGTTAGTGTCTAAAAACAGAGCCCAGGTTATTTACACAAGAAACACCAAG

Alignment

ORF - retro_lcha_50 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.09 %
• Parental protein coverage: 91.94 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPPKDDKKKKDAGKGAKKDKDPVNKSGGKAKK-KKWSKGKVRDKLNNLVLFDKATYDKLYKEVPNYKLIT
          .PPK..KK..DA.K.AK.DK..VNKS.GK.KK.K......VRDKLNNLVL..KATY.KLY.E.PNYKLIT
Retrocopy IPPKGNKK--DAWKSAK-DKCSVNKSSGKVKK<KSCPGQNVRDKLNNLVLSEKATYNKLYRELPNYKLIT

Parental  PAVVSERLKIRGSLARAALQELLNKGMIKLVSKHRAQVIYTRNTK
          PA.V....K...SLA.A.LQELL..GM..LVSK.RAQVIYTRNTK
Retrocopy PAMV----KNKRSLASAVLQELLIEGMVMLVSKNRAQVIYTRNTK

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	1027.91 RPM
DRP000627_kidney	0.00 RPM	1234.29 RPM
DRP000627_pectoral_fin	0.00 RPM	1856.97 RPM
DRP000627_pelvic_fin	0.00 RPM	1759.00 RPM
DRP000627_pharynx	0.00 RPM	695.42 RPM
DRP000627_tail_muscle	0.02 RPM	445.43 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_50 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 23 parental genes, and 132 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000051	5 retrocopies	retro_amel_1654, retro_amel_1765, retro_amel_574, retro_amel_60, retro_amel_684,
Bos taurus	ENSBTAG00000027772	2 retrocopies	retro_btau_203, retro_btau_9,
Canis familiaris	ENSCAFG00000012395	3 retrocopies	retro_cfam_500, retro_cfam_680, retro_cfam_984,
Callithrix jacchus	ENSCJAG00000013691	1 retrocopy	retro_cjac_208,
Cavia porcellus	ENSCPOG00000013298	2 retrocopies	retro_cpor_705, retro_cpor_9,
Equus caballus	ENSECAG00000020978	2 retrocopies	retro_ecab_89, retro_ecab_976,
Felis catus	ENSFCAG00000001151	3 retrocopies	retro_fcat_1792, retro_fcat_601, retro_fcat_903,
Latimeria chalumnae	ENSLACG00000017531	4 retrocopies	retro_lcha_101, retro_lcha_118, retro_lcha_50 , retro_lcha_72,
Loxodonta africana	ENSLAFG00000017117	6 retrocopies	retro_lafr_1074, retro_lafr_270, retro_lafr_387, retro_lafr_431, retro_lafr_478, retro_lafr_90,
Macropus eugenii	ENSMEUG00000014185	3 retrocopies	retro_meug_1181, retro_meug_1562, retro_meug_174,
Microcebus murinus	ENSMICG00000002687	8 retrocopies	retro_mmur_1023, retro_mmur_1514, retro_mmur_229, retro_mmur_308, retro_mmur_387, retro_mmur_425, retro_mmur_485, retro_mmur_688,
Myotis lucifugus	ENSMLUG00000004752	15 retrocopies	retro_mluc_1166, retro_mluc_1482, retro_mluc_1514, retro_mluc_1541, retro_mluc_1665, retro_mluc_1762, retro_mluc_1794, retro_mluc_1947, retro_mluc_2030, retro_mluc_2394, retro_mluc_467, retro_mluc_523, retro_mluc_649, retro_mluc_669, retro_mluc_903,
Macaca mulatta	ENSMMUG00000016894	2 retrocopies	retro_mmul_137, retro_mmul_71,
Mus musculus	ENSMUSG00000009927	15 retrocopies	retro_mmus_128, retro_mmus_1368, retro_mmus_1455, retro_mmus_1760, retro_mmus_1769, retro_mmus_1788, retro_mmus_2375, retro_mmus_2393, retro_mmus_2641, retro_mmus_2700, retro_mmus_2797, retro_mmus_3218, retro_mmus_336, retro_mmus_3523, retro_mmus_880,
Oryctolagus cuniculus	ENSOCUG00000017256	11 retrocopies	retro_ocun_1166, retro_ocun_1231, retro_ocun_1319, retro_ocun_1553, retro_ocun_1761, retro_ocun_291, retro_ocun_298, retro_ocun_548, retro_ocun_623, retro_ocun_856, retro_ocun_978,
Otolemur garnettii	ENSOGAG00000007265	3 retrocopies	retro_ogar_220, retro_ogar_257, retro_ogar_32,
Ochotona princeps	ENSOPRG00000016194	9 retrocopies	retro_opri_1099, retro_opri_1204, retro_opri_256, retro_opri_320, retro_opri_393, retro_opri_493, retro_opri_64, retro_opri_854, retro_opri_873,
Pongo abelii	ENSPPYG00000025915	6 retrocopies	retro_pabe_1889, retro_pabe_1971, retro_pabe_2930, retro_pabe_3507, retro_pabe_71, retro_pabe_94,
Rattus norvegicus	ENSRNOG00000027503	5 retrocopies	retro_rnor_1430, retro_rnor_157, retro_rnor_893, retro_rnor_90, retro_rnor_992,
Sorex araneus	ENSSARG00000002284	4 retrocopies	retro_sara_21, retro_sara_212, retro_sara_43, retro_sara_542,
Ictidomys tridecemlineatus	ENSSTOG00000020783	3 retrocopies	retro_itri_1491, retro_itri_196, retro_itri_87,
Tupaia belangeri	ENSTBEG00000010244	16 retrocopies	retro_tbel_1592, retro_tbel_1823, retro_tbel_1849, retro_tbel_22, retro_tbel_2651, retro_tbel_2744, retro_tbel_3106, retro_tbel_3107, retro_tbel_3499, retro_tbel_374, retro_tbel_3871, retro_tbel_3877, retro_tbel_4239, retro_tbel_4434, retro_tbel_444, retro_tbel_4464,
Vicugna pacos	ENSVPAG00000000266	4 retrocopies	retro_vpac_106, retro_vpac_118, retro_vpac_337, retro_vpac_546,