RetrogeneDB ID: retro_lcha_95

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: JH127916.1:441765..442035(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFS6
• Ensembl ID: ENSLACG00000004625
• Aliases: None
• Description: None

Sequence

>retro_lcha_95
ATGGCTGCAGCCTCGCTGTGGCTAGCGCCCTTCTTACATATCAAGGGTGGATGGGTGGTCTGGATCATCTGCAAAGTGTC
TGCCCAAAACTGTGGGCATCAGAGTACATCTGCAGGGAAGAAAGTCACCCACACTGGGCAGGATCATGATAACAAGGATT
ACAGATGAATTAGATTTGTTGGATGTCAGAAAGAGGTGAATGAAAGTTTTGCCATAGACATATTAGCAGAGGAACCAGTT
ATTGAGGTAAAAGGCAGAGTCAGCTCATGT

Alignment

ORF - retro_lcha_95 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.89 %
• Parental protein coverage: 70.31 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAASCLRLTPFFHIQGGRAVWTICKVSAKNYRHQNVATGEKVTHTGQVYDNKDYRRVRFVGRQKEVNESF
          MAA..L.L.PF.HI.GG..VW.ICKVSA.N..HQ....G.KVTHTGQ..DNKDYR..RFVG.QKEVNESF
Retrocopy MAAASLWLAPFLHIKGGWVVWIICKVSAQNCGHQSTSAGKKVTHTGQDHDNKDYR*IRFVGCQKEVNESF

Parental  AIDLVAEEPVTEVEDRVTSC
          AID..AEEPV.EV..RV.SC
Retrocopy AIDILAEEPVIEVKGRVSSC

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	19.59 RPM
DRP000627_kidney	0.00 RPM	25.23 RPM
DRP000627_pectoral_fin	0.00 RPM	26.74 RPM
DRP000627_pelvic_fin	0.00 RPM	29.01 RPM
DRP000627_pharynx	0.00 RPM	23.02 RPM
DRP000627_tail_muscle	0.00 RPM	17.31 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_95 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 19 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010930	2 retrocopies	retro_amel_213, retro_amel_228,
Bos taurus	ENSBTAG00000009914	2 retrocopies	retro_btau_302, retro_btau_333,
Callithrix jacchus	ENSCJAG00000019382	1 retrocopy	retro_cjac_1552,
Equus caballus	ENSECAG00000021690	3 retrocopies	retro_ecab_701, retro_ecab_838, retro_ecab_917,
Homo sapiens	ENSG00000145494	1 retrocopy	retro_hsap_2838,
Latimeria chalumnae	ENSLACG00000004625	1 retrocopy	retro_lcha_95 ,
Loxodonta africana	ENSLAFG00000005708	1 retrocopy	retro_lafr_5,
Myotis lucifugus	ENSMLUG00000016888	1 retrocopy	retro_mluc_1750,
Macaca mulatta	ENSMMUG00000004447	1 retrocopy	retro_mmul_1473,
Monodelphis domestica	ENSMODG00000001425	1 retrocopy	retro_mdom_207,
Mus musculus	ENSMUSG00000021606	1 retrocopy	retro_mmus_3044,
Nomascus leucogenys	ENSNLEG00000011199	1 retrocopy	retro_nleu_1593,
Oryctolagus cuniculus	ENSOCUG00000004581	2 retrocopies	retro_ocun_1011, retro_ocun_1624,
Pongo abelii	ENSPPYG00000015323	1 retrocopy	retro_pabe_2350,
Pan troglodytes	ENSPTRG00000016706	1 retrocopy	retro_ptro_1924,
Rattus norvegicus	ENSRNOG00000023387	1 retrocopy	retro_rnor_1619,
Rattus norvegicus	ENSRNOG00000049394	1 retrocopy	retro_rnor_1618,
Sarcophilus harrisii	ENSSHAG00000017779	1 retrocopy	retro_shar_176,
Ictidomys tridecemlineatus	ENSSTOG00000003715	1 retrocopy	retro_itri_496,