RetrogeneDB ID: retro_onil_54

Retrocopy location

• Organism: Tilapia (Oreochromis niloticus)
• Coordinates: GL831363.1:838361..838769(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: h3f3a
• Ensembl ID: ENSONIG00000015805
• Aliases: None
• Description: H3 histone, family 3A [Source:ZFIN;Acc:ZDB-GENE-040426-1928]

Sequence

>retro_onil_54
ATGGCCAGGACCAAGCAGACCGCCCGTAAATCCACCGGAGGAAAAGCTCCCAGGAAGCAGCTCGCCACTAAGGCTGCCCG
TAAGAGCGCCCCGGCTACCGGAGGTGTGAAGAAGCCCCACCGTTACAGGCCCGGGACTGTGGCTCTGAGGGAGATCCGCC
GCTATCAGAAATCCACCGAGCTGCTGATCCGTAAGCTGCCGTTCCAGCGCCTGGTTAGGGAGATCGCTCAGGACTTCAAG
ACCGACCTGCGCTTCCAGAGCTCCGCCGTCATGGCTCTGCAGGAGGCTAGCGAGGCTTACCTGGTCGGTCTGTTCGAGGA
CACCAACCTGTGCGCCATCCACGCCAAGAGGGTTACCATTATGCCCAAAGACATCCAGCTGGCCCGCCGCATCCGCGGAG
AGAGGGCT

Alignment

ORF - retro_onil_54 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.06 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQR
          MARTKQTARKSTGGKAPRKQLATKAARKSAP.TGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQR
Retrocopy MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQR

Parental  LVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA
          LVREIAQDFKTDLRFQS.A..ALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA
Retrocopy LVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Oreochromis niloticus was not studied using RNA-Seq expression data.

ChIP-Seq

Oreochromis niloticus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_onil_54 retrocopy.

TSS

Oreochromis niloticus was not studied using FANTOM5 data.

Lab

retro_onil_54 was not experimentally validated.

Homology

Retrocopy orthology:

Oreochromis niloticus 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 17 parental genes, and 78 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000024561	3 retrocopies	retro_btau_156, retro_btau_204, retro_btau_47,
Canis familiaris	ENSCAFG00000004916	2 retrocopies	retro_cfam_1117, retro_cfam_622,
Canis familiaris	ENSCAFG00000016119	4 retrocopies	retro_cfam_168, retro_cfam_1845, retro_cfam_650, retro_cfam_673,
Erinaceus europaeus	ENSEEUG00000013796	1 retrocopy	retro_eeur_2,
Felis catus	ENSFCAG00000003617	4 retrocopies	retro_fcat_1085, retro_fcat_1953, retro_fcat_592, retro_fcat_830,
Felis catus	ENSFCAG00000030424	5 retrocopies	retro_fcat_1251, retro_fcat_1532, retro_fcat_1533, retro_fcat_2011, retro_fcat_674,
Gadus morhua	ENSGMOG00000014306	1 retrocopy	retro_gmor_9,
Macropus eugenii	ENSMEUG00000004090	5 retrocopies	retro_meug_1041, retro_meug_1065, retro_meug_1819, retro_meug_281, retro_meug_573,
Macaca mulatta	ENSMMUG00000031483	9 retrocopies	retro_mmul_108, retro_mmul_147, retro_mmul_201, retro_mmul_213, retro_mmul_215, retro_mmul_286, retro_mmul_337, retro_mmul_346, retro_mmul_7,
Nomascus leucogenys	ENSNLEG00000001577	2 retrocopies	retro_nleu_25, retro_nleu_35,
Otolemur garnettii	ENSOGAG00000024312	11 retrocopies	retro_ogar_1086, retro_ogar_1790, retro_ogar_1863, retro_ogar_2364, retro_ogar_2463, retro_ogar_2581, retro_ogar_2746, retro_ogar_3415, retro_ogar_478, retro_ogar_842, retro_ogar_955,
Otolemur garnettii	ENSOGAG00000025933	14 retrocopies	retro_ogar_1285, retro_ogar_1364, retro_ogar_1449, retro_ogar_1575, retro_ogar_1576, retro_ogar_2200, retro_ogar_2316, retro_ogar_2449, retro_ogar_2634, retro_ogar_3235, retro_ogar_42, retro_ogar_733, retro_ogar_937, retro_ogar_952,
Oreochromis niloticus	ENSONIG00000015805	7 retrocopies	retro_onil_45, retro_onil_47, retro_onil_51, retro_onil_54 , retro_onil_61, retro_onil_65, retro_onil_69,
Oreochromis niloticus	ENSONIG00000019975	5 retrocopies	retro_onil_41, retro_onil_46, retro_onil_56, retro_onil_60, retro_onil_63,
Pongo abelii	ENSPPYG00000008636	1 retrocopy	retro_pabe_2662,
Pteropus vampyrus	ENSPVAG00000008459	2 retrocopies	retro_pvam_218, retro_pvam_52,
Sus scrofa	ENSSSCG00000023971	2 retrocopies	retro_sscr_31, retro_sscr_712,