RetrogeneDB ID: retro_ggal_19

Retrocopy location

• Organism: Chicken (Gallus gallus)
• Coordinates: 8:8780988..8781218(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MINOS1
• Ensembl ID: ENSGALG00000004039
• Aliases: MINOS1, C1orf151
• Description: None

Sequence

>retro_ggal_19
ATGGCATTGGAGGGCGAGCTGGGCAGGAATTGGGATCATTGTCTGGCAGACTCCGCTGTCAAGCTGGGTGCTAGAATTGG
GTTAGAAATTGTTTTCTCAGTCATCTCCTTCAAAAGAAAGACATAGCCTATTGCATTTGGGTCTGGGATGGGGTTAGGAA
TGGCTTATTTCAATTGTCAACATGACTTCCTATCTCCATATCTTCTCCATGGTAATTTGTAAAAGAGAAA

Alignment

ORF - retro_ggal_19 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.33 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MASEGELGRKWDRCLADSAVKLGAGFGLGIVFSVIFFKRKTWPIAFGSGMGLGMAYSNCQHDFQSPYLLH
          MA.EGELGR.WD.CLADSAVKLGA..GL.IVFSVI.FKRKT.PIAFGSGMGLGMAY.NCQHDF.SPYLLH
Retrocopy MALEGELGRNWDHCLADSAVKLGARIGLEIVFSVISFKRKT*PIAFGSGMGLGMAYFNCQHDFLSPYLLH

Parental  GK-FVKEQ
          G..FVKE.
Retrocopy GN<FVKEK

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
SRP007412_brain	0.00 RPM	27.72 RPM
SRP007412_cerebellum	0.00 RPM	23.83 RPM
SRP007412_heart	0.00 RPM	76.35 RPM
SRP007412_kidney	0.00 RPM	50.31 RPM
SRP007412_liver	0.00 RPM	23.23 RPM
SRP007412_testis	0.00 RPM	36.62 RPM

ChIP-Seq

Gallus gallus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ggal_19 retrocopy.

TSS

Gallus gallus was not studied using FANTOM5 data.

Lab

retro_ggal_19 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggal_19 has 0 orthologous retrocopies within neognath group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003110	3 retrocopies	retro_amel_1685, retro_amel_502, retro_amel_689,
Callithrix jacchus	ENSCJAG00000006709	1 retrocopy	retro_cjac_2070,
Echinops telfairi	ENSETEG00000010942	5 retrocopies	retro_etel_1360, retro_etel_1463, retro_etel_171, retro_etel_459, retro_etel_978,
Felis catus	ENSFCAG00000003066	2 retrocopies	retro_fcat_1448, retro_fcat_739,
Homo sapiens	ENSG00000173436	3 retrocopies	retro_hsap_1857, retro_hsap_2761, retro_hsap_2948,
Gallus gallus	ENSGALG00000004039	1 retrocopy	retro_ggal_19 ,
Gorilla gorilla	ENSGGOG00000007347	4 retrocopies	retro_ggor_1920, retro_ggor_2042, retro_ggor_2154, retro_ggor_979,
Loxodonta africana	ENSLAFG00000016199	1 retrocopy	retro_lafr_825,
Macaca mulatta	ENSMMUG00000005855	2 retrocopies	retro_mmul_1268, retro_mmul_1949,
Mus musculus	ENSMUSG00000050608	1 retrocopy	retro_mmus_2357,
Nomascus leucogenys	ENSNLEG00000007867	2 retrocopies	retro_nleu_1297, retro_nleu_665,
Pongo abelii	ENSPPYG00000001788	3 retrocopies	retro_pabe_1513, retro_pabe_2251, retro_pabe_2445,
Pan troglodytes	ENSPTRG00000000269	2 retrocopies	retro_ptro_1868, retro_ptro_2050,
Rattus norvegicus	ENSRNOG00000042696	2 retrocopies	retro_rnor_16, retro_rnor_2460,
Sus scrofa	ENSSSCG00000028414	1 retrocopy	retro_sscr_1171,
Tupaia belangeri	ENSTBEG00000004024	1 retrocopy	retro_tbel_4339,
Tarsius syrichta	ENSTSYG00000002903	1 retrocopy	retro_tsyr_825,
Vicugna pacos	ENSVPAG00000011525	1 retrocopy	retro_vpac_607,