RetrogeneDB ID: retro_onil_46

Retrocopy location

• Organism: Tilapia (Oreochromis niloticus)
• Coordinates: GL831231.1:1058846..1059254(-)
• Located in intron of: ENSONIG00000007436

Retrocopy information

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

Parental gene information

• Parental gene symbol: H3F3B
• Ensembl ID: ENSONIG00000019975
• Aliases: None
• Description: H3 histone, family 3B (H3.3B) [Source:HGNC Symbol;Acc:4765]

Sequence

>retro_onil_46
ATGGCAAGAACCAAGCAGACCGCTCGCAAGTCTACTGGCGGCAAAGCTCCCAGGAAGCAGCTGGCCACCAAGGCCGCTCG
TAAGAGCGCCCCGGCCACCGGAGGCGTCAAGAAGCCTCACCGTTACAGGCCCGGTACCGTGGCTCTGCGTGAGATCCGCC
GTTACCAGAAATCCACCGAGCTGCTGATCCGCAAGCTGCCCTTCCAGCGCCTGGTCCGCGAGATCGCCCAGGACTTCAAG
ACCGACCTGCGCTTCCAGAGCTCTGCTGTCATGGCTCTGCAGGAGGCCAGCGAGGCTTACCTGGTCGGACTCTTCGAGGA
CACCAACCTGTGCGCCATCCACGCCAAGAGGGTCACCATCATGCCCAAAGACATCCAGCTGGCTCGTCGCATCCGCGGAG
AGAGAGCT

Alignment

ORF - retro_onil_46 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_46 retrocopy.

TSS

Oreochromis niloticus was not studied using FANTOM5 data.

Lab

retro_onil_46 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 81 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012702	10 retrocopies	retro_cjac_145, retro_cjac_198, retro_cjac_201, retro_cjac_224, retro_cjac_235, retro_cjac_238, retro_cjac_307, retro_cjac_334, retro_cjac_366, retro_cjac_68,
Dasypus novemcinctus	ENSDNOG00000024843	2 retrocopies	retro_dnov_1624, retro_dnov_775,
Equus caballus	ENSECAG00000006904	1 retrocopy	retro_ecab_916,
Equus caballus	ENSECAG00000016948	1 retrocopy	retro_ecab_266,
Latimeria chalumnae	ENSLACG00000004118	1 retrocopy	retro_lcha_104,
Loxodonta africana	ENSLAFG00000008083	3 retrocopies	retro_lafr_837, retro_lafr_959, retro_lafr_99,
Loxodonta africana	ENSLAFG00000021624	4 retrocopies	retro_lafr_172, retro_lafr_410, retro_lafr_546, retro_lafr_832,
Microcebus murinus	ENSMICG00000002139	2 retrocopies	retro_mmur_36, retro_mmur_371,
Myotis lucifugus	ENSMLUG00000015447	10 retrocopies	retro_mluc_146, retro_mluc_1571, retro_mluc_2286, retro_mluc_2344, retro_mluc_2364, retro_mluc_246, retro_mluc_2468, retro_mluc_2500, retro_mluc_392, retro_mluc_613,
Mustela putorius furo	ENSMPUG00000004555	4 retrocopies	retro_mputfur_389, retro_mputfur_82, retro_mputfur_99, retro_mputfur_990,
Oryctolagus cuniculus	ENSOCUG00000024644	2 retrocopies	retro_ocun_185, retro_ocun_217,
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,
Ictidomys tridecemlineatus	ENSSTOG00000024226	8 retrocopies	retro_itri_315, retro_itri_449, retro_itri_465, retro_itri_505, retro_itri_649, retro_itri_695, retro_itri_764, retro_itri_771,
Tupaia belangeri	ENSTBEG00000006177	13 retrocopies	retro_tbel_110, retro_tbel_1274, retro_tbel_15, retro_tbel_170, retro_tbel_2335, retro_tbel_3341, retro_tbel_3342, retro_tbel_3820, retro_tbel_391, retro_tbel_487, retro_tbel_592, retro_tbel_783, retro_tbel_978,
Tupaia belangeri	ENSTBEG00000016171	7 retrocopies	retro_tbel_3459, retro_tbel_3605, retro_tbel_3824, retro_tbel_3856, retro_tbel_4243, retro_tbel_4350, retro_tbel_674,