RetrogeneDB ID: retro_cjac_163

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 19:17323082..17323316(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000021903
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000019788
• Aliases: None
• Description: None

Sequence

>retro_cjac_163
ATGCCCAAGTGCCCCAAGTGCGACAAGGAGGTGTACTTCGCTGAGAGGGTGACCTCTCTGGGCAAGGACTGGCATCGGCC
TTGCCTGAAGTGCGAGAAATGTGGGAAGACGCTGACCTCCGGCGGCCACGCTGAGCACGAAGGCAAACCCTACTGCAACC
ATCCCTGCTACTCCGCCATGTTTGGGCCTAAAGGCTTTGGGCGGGGTGGAGCTGAGAGCCACACTTTCAAGTAA

Alignment

ORF - retro_cjac_163 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.7 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPKCPKCEKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFGPKGFGRGG
          MPKCPKC.KEVYFAERVTSLGKDWHRPCLKCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFGPKGFGRGG
Retrocopy MPKCPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFGPKGFGRGG

Parental  AESHTFK
          AESHTFK
Retrocopy AESHTFK

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	0.04 RPM	21.17 RPM
SRP051959_heart	0.04 RPM	12.31 RPM
SRP051959_kidney	0.00 RPM	4.81 RPM
SRP051959_liver	0.00 RPM	3.96 RPM
SRP051959_lung	0.03 RPM	16.01 RPM
SRP051959_lymph_node	0.11 RPM	18.42 RPM
SRP051959_skeletal_muscle	0.00 RPM	2.99 RPM
SRP051959_spleen	0.04 RPM	7.54 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_163 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_163 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_163 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000047229	1 retrocopy	retro_btau_488,
Callithrix jacchus	ENSCJAG00000019153	6 retrocopies	retro_cjac_1266, retro_cjac_1285, retro_cjac_1384, retro_cjac_1555, retro_cjac_2919, retro_cjac_3150,
Callithrix jacchus	ENSCJAG00000019788	1 retrocopy	retro_cjac_163 ,
Dipodomys ordii	ENSDORG00000001365	1 retrocopy	retro_dord_70,
Homo sapiens	ENSG00000213145	1 retrocopy	retro_hsap_2550,
Gorilla gorilla	ENSGGOG00000027381	1 retrocopy	retro_ggor_3,
Macropus eugenii	ENSMEUG00000001631	1 retrocopy	retro_meug_93,
Macaca mulatta	ENSMMUG00000007158	2 retrocopies	retro_mmul_1479, retro_mmul_553,
Pongo abelii	ENSPPYG00000006209	1 retrocopy	retro_pabe_114,
Pan troglodytes	ENSPTRG00000033768	1 retrocopy	retro_ptro_43,
Pteropus vampyrus	ENSPVAG00000014240	1 retrocopy	retro_pvam_1304,
Rattus norvegicus	ENSRNOG00000027990	2 retrocopies	retro_rnor_2590, retro_rnor_2599,
Sarcophilus harrisii	ENSSHAG00000000807	1 retrocopy	retro_shar_341,
Tursiops truncatus	ENSTTRG00000004063	1 retrocopy	retro_ttru_1367,