RetrogeneDB ID: retro_lcha_100

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: JH128138.1:476415..476886(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFB10
• Ensembl ID: ENSLACG00000013152
• Aliases: None
• Description: None

Sequence

>retro_lcha_100
AAACCTCCTTGCTGGACCCCGGTGGTAAAGAAGATGAACCTCTTCAACCAGGTTGCCATCATAACCAACATACTTTATTA
TGTGATGGATTGGTCAGTGACTTACTTTCAAGAGTGGATGGAACACCAGCACTCAAGGAACAAGTTTTACTACTATCACC
ATCAGTTCTGCTGTGTGCCAGACTTGACAGAACGTTAGCTGGAAGATTACCAATGCCAGTATGAGGCTGAGATGCAATGG
AGGAAAAACCACAAAGTGGATCAAAAGATTGTGACAATCATTCAGGATATGTTGAAGGCCTGCCAAGAAAGAGAAGGAAA
TAGCTCCCTGCAGAGCTGTGCAAAGGAGATGGAACAACTCCAACCATTTGCAAAGGTCTACCAATTCAGATATGGAGACC
TTGGTGCATATGGTAATGCTAGAAAGTGCATTATGAAGCAAAAGCACAGAATGATCAAAGAGAGAGCAAAG

Alignment

ORF - retro_lcha_100 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.89 %
• Parental protein coverage: 90.8 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EPPRRTPVVKKETNLPNPASIATNIFYYAVDQPVTYFREWMERQHSRNKFYYYHRQFRRVPDLTECQTDD
          .PP..TPVVKK..NL.N...I.TNI.YY..D..VTYF.EWME.QHSRNKFYYYH.QF..VPDLTE....D
Retrocopy KPPCWTPVVKK-MNLFNQVAIITNILYYVMDWSVTYFQEWMEHQHSRNKFYYYHHQFCCVPDLTER*LED

Parental  YLCLYEAEMQWRRDHKVDQEIVKIVQDRLKACQQREGSSYLQNCAKEVEQFRQVAKGYQSRYGDLGAYGS
          Y.C.YEAEMQWR..HKVDQ.IV.I.QD.LKACQ.REG.S.LQ.CAKE.EQ....AK.YQ.RYGDLGAYG.
Retrocopy YQCQYEAEMQWRKNHKVDQKIVTIIQDMLKACQEREGNSSLQSCAKEMEQLQPFAKVYQFRYGDLGAYGN

Parental  ARKCLMKQKHRMIKEREK
          ARKC.MKQKHRMIKER.K
Retrocopy ARKCIMKQKHRMIKERAK

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	27.70 RPM
DRP000627_kidney	0.00 RPM	48.42 RPM
DRP000627_pectoral_fin	0.00 RPM	51.34 RPM
DRP000627_pelvic_fin	0.00 RPM	56.43 RPM
DRP000627_pharynx	0.00 RPM	30.40 RPM
DRP000627_tail_muscle	0.00 RPM	22.41 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_100 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 13 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000019476	1 retrocopy	retro_cfam_1861,
Echinops telfairi	ENSETEG00000017154	1 retrocopy	retro_etel_1955,
Felis catus	ENSFCAG00000011738	1 retrocopy	retro_fcat_307,
Homo sapiens	ENSG00000140990	2 retrocopies	retro_hsap_1573, retro_hsap_3801,
Gorilla gorilla	ENSGGOG00000009367	2 retrocopies	retro_ggor_1198, retro_ggor_2555,
Latimeria chalumnae	ENSLACG00000013152	1 retrocopy	retro_lcha_100 ,
Macaca mulatta	ENSMMUG00000029268	1 retrocopy	retro_mmul_2218,
Mus musculus	ENSMUSG00000040048	1 retrocopy	retro_mmus_2566,
Nomascus leucogenys	ENSNLEG00000008867	1 retrocopy	retro_nleu_1740,
Pongo abelii	ENSPPYG00000006974	2 retrocopies	retro_pabe_1297, retro_pabe_3106,
Pan troglodytes	ENSPTRG00000007618	2 retrocopies	retro_ptro_1060, retro_ptro_2578,
Rattus norvegicus	ENSRNOG00000014568	1 retrocopy	retro_rnor_1056,
Sus scrofa	ENSSSCG00000030328	1 retrocopy	retro_sscr_689,