RetrogeneDB ID: retro_lcha_21

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: AFYH01277154.1:717..1071(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPE
• Ensembl ID: ENSLACG00000002800
• Aliases: None
• Description: Ribulose-phosphate 3-epimerase [Source:UniProtKB/TrEMBL;Acc:H3A0F4]

Sequence

>retro_lcha_21
ATCAAAGAAAAAGAAAATCCTGGAGCTCTTATTAAAGACATCTGGGAGAATGGTATGAAGGTGGGTCTGGCTGTCCAACC
AGGAACAACAGTGGAGTATTTGGCTCCATGGGCTAATCAAATCAATATGGTATTGGTTATGACAGTGGAACCAGGGTTTG
GCGGTGCAACGTTCATGGAAGGTATGATGCCAAAGGTTAACTGGTTAAGAACAGAGTTTCCTTCTTTGGATATAGAAGTA
GATGGCGGAGTGGGTGTTGATATAATTAGTAAATGTGCAGAAGGTGTTGCCAACATGATTGTATCTGGCAGTGCAGTTAT
GAAAAGTGATGACTTCAGATCGGTGATGAACGTT

Alignment

ORF - retro_lcha_21 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.36 %
• Parental protein coverage: 50.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LEATDNPGALIKDIRENSMKVGLAIKPGTTVEYLAPWANQIDMALVMTVEPGFGGQTFMEDMMPKVSWLR
          .....NPGALIKDI.EN.MKVGLA..PGTTVEYLAPWANQI.M.LVMTVEPGFGG.TFME.MMPKV.WLR
Retrocopy IKEKENPGALIKDIWENGMKVGLAVQPGTTVEYLAPWANQINMVLVMTVEPGFGGATFMEGMMPKVNWLR

Parental  TQFPSLDIEVDGGVGPDTISKCAEAGANMIVSGSAVMKSDDPRSVINL
          T.FPSLDIEVDGGVG.D.ISKCAE..ANMIVSGSAVMKSDD.RSV.N.
Retrocopy TEFPSLDIEVDGGVGVDIISKCAEGVANMIVSGSAVMKSDDFRSVMNV

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	6.47 RPM
DRP000627_kidney	0.00 RPM	5.16 RPM
DRP000627_pectoral_fin	0.00 RPM	8.46 RPM
DRP000627_pelvic_fin	0.00 RPM	13.60 RPM
DRP000627_pharynx	0.00 RPM	5.22 RPM
DRP000627_tail_muscle	0.00 RPM	4.27 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_21 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 24 parental genes, and 61 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004965	3 retrocopies	retro_amel_1327, retro_amel_1363, retro_amel_827,
Bos taurus	ENSBTAG00000047806	2 retrocopies	retro_btau_343, retro_btau_815,
Canis familiaris	ENSCAFG00000013811	3 retrocopies	retro_cfam_1441, retro_cfam_1596, retro_cfam_1623,
Choloepus hoffmanni	ENSCHOG00000001110	5 retrocopies	retro_chof_1534, retro_chof_2386, retro_chof_392, retro_chof_492, retro_chof_574,
Callithrix jacchus	ENSCJAG00000010822	2 retrocopies	retro_cjac_1199, retro_cjac_1560,
Dasypus novemcinctus	ENSDNOG00000003193	1 retrocopy	retro_dnov_789,
Equus caballus	ENSECAG00000000002	3 retrocopies	retro_ecab_245, retro_ecab_446, retro_ecab_562,
Homo sapiens	ENSG00000197713	5 retrocopies	retro_hsap_133, retro_hsap_2553, retro_hsap_2620, retro_hsap_3330, retro_hsap_620,
Latimeria chalumnae	ENSLACG00000002800	1 retrocopy	retro_lcha_21 ,
Loxodonta africana	ENSLAFG00000014127	2 retrocopies	retro_lafr_675, retro_lafr_729,
Microcebus murinus	ENSMICG00000009953	4 retrocopies	retro_mmur_1380, retro_mmur_268, retro_mmur_393, retro_mmur_713,
Macaca mulatta	ENSMMUG00000010513	2 retrocopies	retro_mmul_366, retro_mmul_618,
Monodelphis domestica	ENSMODG00000015827	6 retrocopies	retro_mdom_1181, retro_mdom_1676, retro_mdom_449, retro_mdom_490, retro_mdom_505, retro_mdom_667,
Mustela putorius furo	ENSMPUG00000007948	2 retrocopies	retro_mputfur_1066, retro_mputfur_1280,
Nomascus leucogenys	ENSNLEG00000007172	3 retrocopies	retro_nleu_2263, retro_nleu_448, retro_nleu_638,
Oryctolagus cuniculus	ENSOCUG00000016995	1 retrocopy	retro_ocun_768,
Otolemur garnettii	ENSOGAG00000002778	1 retrocopy	retro_ogar_2673,
Pongo abelii	ENSPPYG00000013132	4 retrocopies	retro_pabe_1052, retro_pabe_1878, retro_pabe_2340, retro_pabe_555,
Pteropus vampyrus	ENSPVAG00000014452	2 retrocopies	retro_pvam_217, retro_pvam_636,
Sus scrofa	ENSSSCG00000016152	1 retrocopy	retro_sscr_825,
Ictidomys tridecemlineatus	ENSSTOG00000010322	1 retrocopy	retro_itri_1750,
Tarsius syrichta	ENSTSYG00000003304	5 retrocopies	retro_tsyr_113, retro_tsyr_1153, retro_tsyr_1663, retro_tsyr_2129, retro_tsyr_546,
Tursiops truncatus	ENSTTRG00000000908	1 retrocopy	retro_ttru_158,
Vicugna pacos	ENSVPAG00000011585	1 retrocopy	retro_vpac_91,