RetrogeneDB ID: retro_lcha_49

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: JH126937.1:737923..738237(-)
• Located in intron of: ENSLACG00000006141

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS25
• Ensembl ID: ENSLACG00000009006
• Aliases: None
• Description: None

Sequence

>retro_lcha_49
TTCAGAAAAAGAACACCTTCGCCATTTCTAATGTCTTGTTTTGATGACGGTGACCAAATTTTGGTTGGCATGGAAGGCAA
GGACCACGACAAAATTATATTGAGAAAATCATGGGCAAAAGCCAAGAGGTTCTTCATGCAGAGAAGCAGGCAAGGATGGT
GTGCTCCAACCCAGCCACCTTCAGGCCCTAAAAGTACTGTCTGCGAGAAGACATGTGTGGGGCGGAGGGACCGGTCCCCT
GTACTGGCTTAGTGCCCTTGCCAAAGAAAAGGGCCAGAAAATCCCAGGCGCCTCAGAAAGAATCCACAGAAGTT

Alignment

ORF - retro_lcha_49 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.48 %
• Parental protein coverage: 61.85 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FKNMTPSPFLKFYLDDGEQVLVDVEGKNHTEIYQHVKKLLGKSQ-EVLHAEEQAKMVHSNPANFGPKKYC
          F...TPSPFL....DDG.Q.LV..EGK.H..I.....K...K...EVLHAE.QA.MV.SNPA.F.P.KYC
Retrocopy FRKRTPSPFLMSCFDDGDQILVGMEGKDHDKII--LRKSWAKAK<EVLHAEKQARMVCSNPATFRP*KYC

Parental  LRECMCEVEGQVPCPAFVPLPREMTGKYRNAQKESTEV
          LRE.MC..EG.VPC...VPLP.....K....QKESTEV
Retrocopy LREDMCGAEGPVPCTGLVPLPKKRARKSQAPQKESTEV

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	3.21 RPM
DRP000627_kidney	0.00 RPM	4.88 RPM
DRP000627_pectoral_fin	0.00 RPM	3.93 RPM
DRP000627_pelvic_fin	0.00 RPM	5.47 RPM
DRP000627_pharynx	0.00 RPM	2.98 RPM
DRP000627_tail_muscle	0.00 RPM	2.17 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_49 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 20 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004349	1 retrocopy	retro_amel_1861,
Canis familiaris	ENSCAFG00000028683	1 retrocopy	retro_cfam_2200,
Callithrix jacchus	ENSCJAG00000017160	1 retrocopy	retro_cjac_3303,
Echinops telfairi	ENSETEG00000008261	2 retrocopies	retro_etel_1144, retro_etel_1227,
Felis catus	ENSFCAG00000027687	1 retrocopy	retro_fcat_2014,
Homo sapiens	ENSG00000131368	1 retrocopy	retro_hsap_1127,
Gorilla gorilla	ENSGGOG00000011005	1 retrocopy	retro_ggor_880,
Latimeria chalumnae	ENSLACG00000009006	1 retrocopy	retro_lcha_49 ,
Loxodonta africana	ENSLAFG00000022178	1 retrocopy	retro_lafr_1068,
Macaca mulatta	ENSMMUG00000005157	2 retrocopies	retro_mmul_1946, retro_mmul_874,
Mustela putorius furo	ENSMPUG00000017248	1 retrocopy	retro_mputfur_1608,
Nomascus leucogenys	ENSNLEG00000005218	1 retrocopy	retro_nleu_184,
Oryctolagus cuniculus	ENSOCUG00000006984	1 retrocopy	retro_ocun_1040,
Ochotona princeps	ENSOPRG00000009370	3 retrocopies	retro_opri_288, retro_opri_690, retro_opri_951,
Pongo abelii	ENSPPYG00000013409	1 retrocopy	retro_pabe_932,
Pelodiscus sinensis	ENSPSIG00000008882	1 retrocopy	retro_psin_36,
Pan troglodytes	ENSPTRG00000014658	1 retrocopy	retro_ptro_678,
Rattus norvegicus	ENSRNOG00000010912	1 retrocopy	retro_rnor_1184,
Ictidomys tridecemlineatus	ENSSTOG00000027997	1 retrocopy	retro_itri_984,
Tursiops truncatus	ENSTTRG00000009881	1 retrocopy	retro_ttru_140,