RetrogeneDB ID: retro_cjac_1978

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:182845522..182845819(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000009945
• Aliases: None
• Description: None

Sequence

>retro_cjac_1978
GAAGACCTGAAAGATCCAGAAGTATTCCAGGTCCAGATGCAGCTGATGGAAGCCATGTTCGGCCGGGACCGATGTCAAAT
CCCTTACATCGAGCAGGTGAGCAAGGCTATGCTCGAGCTGAAGGCTCTGGAGTCTCCAGACTTCACCGAGGTTGTGGTTT
ACGGCTCCTATATATACAAGCTCCGAGCCAAGTGGATGCTCCAGTCTATGGCTGAGTGGCACTGCCAGCGCCAGGAGCGA
GGGATGCTCAAACTTGAGAAAGCCATGAATGCCCTCGAACTGAGCCCTTGGATGAAC

Alignment

ORF - retro_cjac_1978 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.0 %
• Parental protein coverage: 85.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EDLKDPEVFQVQTRLLEAMFAGRDGCRIPYIEQVSKAMLELKALESPDFTEVVVYGSYIYKLRAKWMLQS
          EDLKDPEVFQVQ..L.EAMF.GRD.C.IPYIEQVSKAMLELKALESPDFTEVVVYGSYIYKLRAKWMLQS
Retrocopy EDLKDPEVFQVQMQLMEAMF-GRDRCQIPYIEQVSKAMLELKALESPDFTEVVVYGSYIYKLRAKWMLQS

Parental  MAEWHRQRQERGMLKLEEAMNALELSPWMN
          MAEWH.QRQERGMLKLE.AMNALELSPWMN
Retrocopy MAEWHCQRQERGMLKLEKAMNALELSPWMN

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
SRP051959_colon	0.00 RPM	0.00 RPM
SRP051959_heart	0.00 RPM	0.16 RPM
SRP051959_kidney	0.00 RPM	0.02 RPM
SRP051959_liver	0.00 RPM	0.00 RPM
SRP051959_lung	0.00 RPM	0.07 RPM
SRP051959_lymph_node	0.00 RPM	0.02 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.00 RPM
SRP051959_spleen	0.00 RPM	0.04 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1978 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1978 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1978 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000002647	2 retrocopies	retro_cfam_1216, retro_cfam_524,
Choloepus hoffmanni	ENSCHOG00000012338	1 retrocopy	retro_chof_2495,
Callithrix jacchus	ENSCJAG00000009945	3 retrocopies	retro_cjac_1978 , retro_cjac_62, retro_cjac_85,
Dasypus novemcinctus	ENSDNOG00000011544	4 retrocopies	retro_dnov_115, retro_dnov_15, retro_dnov_2318, retro_dnov_53,
Dipodomys ordii	ENSDORG00000000378	2 retrocopies	retro_dord_324, retro_dord_690,
Homo sapiens	ENSG00000203909	1 retrocopy	retro_hsap_2067,
Gorilla gorilla	ENSGGOG00000012001	1 retrocopy	retro_ggor_1489,
Myotis lucifugus	ENSMLUG00000004463	1 retrocopy	retro_mluc_1051,
Macaca mulatta	ENSMMUG00000000417	1 retrocopy	retro_mmul_1409,
Mus musculus	ENSMUSG00000060461	7 retrocopies	retro_mmus_127, retro_mmus_1280, retro_mmus_1537, retro_mmus_1666, retro_mmus_2557, retro_mmus_3415, retro_mmus_58,
Pongo abelii	ENSPPYG00000016771	1 retrocopy	retro_pabe_1680,
Pan troglodytes	ENSPTRG00000029547	1 retrocopy	retro_ptro_1380,
Rattus norvegicus	ENSRNOG00000000199	3 retrocopies	retro_rnor_106, retro_rnor_28, retro_rnor_76,
Sus scrofa	ENSSSCG00000004283	2 retrocopies	retro_sscr_190, retro_sscr_487,
Ictidomys tridecemlineatus	ENSSTOG00000005326	2 retrocopies	retro_itri_199, retro_itri_703,