RetrogeneDB ID: retro_lcha_69

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: JH127193.1:190666..190939(-)
• Located in intron of: ENSLACG00000003609

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPDPF
• Ensembl ID: ENSLACG00000002835
• Aliases: None
• Description: None

Sequence

>retro_lcha_69
AGCAGCCCACTCATTGCAGCCCACAACTCTTACAGGAGACATCTGGGGGTCCACCTCCAGTGACATAGCTCCTGTAGAAG
CATTGAGTATTCTAGAGAAGTCACTCCTCACCCTGTGGGTCTGCTGAAGTCAAACCCTGGTTACTGGTAGGCCAGTGTCT
TTTTCAAGAAGCAAAACCATCTGGCCGTGATAACTGTGCCAGTGTCCTCAGAGATCCCTAGATCCATAAGCTTGATTAAC
AACAGGATGGTCTGTGGTTTGACTCAGGAAGTG

Alignment

ORF - retro_lcha_69 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.85 %
• Parental protein coverage: 78.95 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SGSLIATHDYYRRRLGSTSS-NSSCGSIEYSGEVIPHPPGLPKSDPGHWWASFFFGKPNHPTMTTVSEFP
          S..LIA.H..YRR.LG......SSC.SIEYS.EV.PHP.GL.KS.PG.W.AS.FF.K.NH....TV....
Retrocopy SSPLIAAHNSYRRHLGVHLQ*HSSCRSIEYSREVTPHPVGLLKSNPGYW*ASVFFKKQNHLAVITVPVSS

Parental  ESSKSVSVVNGKINCGLAQEV
          E...S.S..N....CGL.QEV
Retrocopy EIPRSISLINNRMVCGLTQEV

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	368.80 RPM
DRP000627_kidney	0.00 RPM	343.48 RPM
DRP000627_pectoral_fin	0.00 RPM	375.82 RPM
DRP000627_pelvic_fin	0.00 RPM	587.35 RPM
DRP000627_pharynx	0.00 RPM	293.20 RPM
DRP000627_tail_muscle	0.00 RPM	293.35 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_69 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 16 parental genes, and 56 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000031800	7 retrocopies	retro_btau_1339, retro_btau_1538, retro_btau_1606, retro_btau_1817, retro_btau_1857, retro_btau_385, retro_btau_54,
Equus caballus	ENSECAG00000009413	1 retrocopy	retro_ecab_477,
Felis catus	ENSFCAG00000024386	14 retrocopies	retro_fcat_1018, retro_fcat_1061, retro_fcat_128, retro_fcat_1293, retro_fcat_1581, retro_fcat_1669, retro_fcat_1685, retro_fcat_194, retro_fcat_308, retro_fcat_325, retro_fcat_355, retro_fcat_440, retro_fcat_711, retro_fcat_789,
Homo sapiens	ENSG00000125534	1 retrocopy	retro_hsap_3205,
Latimeria chalumnae	ENSLACG00000002835	1 retrocopy	retro_lcha_69 ,
Loxodonta africana	ENSLAFG00000026496	2 retrocopies	retro_lafr_1082, retro_lafr_251,
Macaca mulatta	ENSMMUG00000006064	2 retrocopies	retro_mmul_2020, retro_mmul_41,
Monodelphis domestica	ENSMODG00000016871	2 retrocopies	retro_mdom_1325, retro_mdom_222,
Mustela putorius furo	ENSMPUG00000008301	12 retrocopies	retro_mputfur_1039, retro_mputfur_1097, retro_mputfur_1247, retro_mputfur_1282, retro_mputfur_1312, retro_mputfur_1327, retro_mputfur_1355, retro_mputfur_347, retro_mputfur_526, retro_mputfur_665, retro_mputfur_788, retro_mputfur_928,
Mus musculus	ENSMUSG00000016344	3 retrocopies	retro_mmus_1224, retro_mmus_658, retro_mmus_815,
Nomascus leucogenys	ENSNLEG00000010068	3 retrocopies	retro_nleu_1154, retro_nleu_1270, retro_nleu_1339,
Otolemur garnettii	ENSOGAG00000008810	2 retrocopies	retro_ogar_1797, retro_ogar_1912,
Pan troglodytes	ENSPTRG00000013739	1 retrocopy	retro_ptro_2243,
Rattus norvegicus	ENSRNOG00000012722	1 retrocopy	retro_rnor_752,
Sarcophilus harrisii	ENSSHAG00000018338	3 retrocopies	retro_shar_637, retro_shar_640, retro_shar_733,
Ictidomys tridecemlineatus	ENSSTOG00000007808	1 retrocopy	retro_itri_1363,