RetrogeneDB ID: retro_cjac_150

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 10:76218171..76218477(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000022927
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000003916
• Aliases: None
• Description: None

Sequence

>retro_cjac_150
ATGGAGCGCCGGGATAAAGCGGCGCTGAACGCACTGCAACCTCCTGAGTTCAGAAATGAAAGTTCATTAGCATCTACGCT
GAAGACGCTCCTGTTCTTCACAGCTTTAATGATCACTGTACCTGTTGGGTTATATTTCACAACTAAATCTTATATATTTG
AAGGCGCCCTTGGGATGTCCAACAGGGACAGCTATTTTTATGCTGCTATTGTTGCAGTAGTCGCCGTCCATGTGGTGCTG
GCCCTCTTTGTGTATGTGGCCTGGAATGAAGGCTCACGACAGTGGCGTGAAGGCAAACAGGATTAA

Alignment

ORF - retro_cjac_150 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.02 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MERPDKAALNALQPPEFRNESSLASTLKTLLFFTALMITVPIGLYFTTKSYIFEGALGMSNRDSYFYAAI
          MER.DKAALNALQPPEFRNESSLASTLKTLLFFTALMITVP.GLYFTTKSYIFEGALGMSNRDSYFYAAI
Retrocopy MERRDKAALNALQPPEFRNESSLASTLKTLLFFTALMITVPVGLYFTTKSYIFEGALGMSNRDSYFYAAI

Parental  VAVVAVHVVLALFVYVAWNEGSRQWREGKQD
          VAVVAVHVVLALFVYVAWNEGSRQWREGKQD
Retrocopy VAVVAVHVVLALFVYVAWNEGSRQWREGKQD

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	0.31 RPM	6.48 RPM
SRP051959_heart	0.21 RPM	8.96 RPM
SRP051959_kidney	0.09 RPM	10.63 RPM
SRP051959_liver	0.11 RPM	5.83 RPM
SRP051959_lung	0.10 RPM	9.45 RPM
SRP051959_lymph_node	0.09 RPM	13.04 RPM
SRP051959_skeletal_muscle	0.15 RPM	9.02 RPM
SRP051959_spleen	0.04 RPM	11.87 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_150 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_150 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_150 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006296	1 retrocopy	retro_btau_1106,
Callithrix jacchus	ENSCJAG00000003916	1 retrocopy	retro_cjac_150 ,
Dasypus novemcinctus	ENSDNOG00000008426	1 retrocopy	retro_dnov_504,
Homo sapiens	ENSG00000160131	1 retrocopy	retro_hsap_3724,
Macaca mulatta	ENSMMUG00000009034	1 retrocopy	retro_mmul_1693,
Mus musculus	ENSMUSG00000073131	2 retrocopies	retro_mmus_116, retro_mmus_3675,
Nomascus leucogenys	ENSNLEG00000013711	1 retrocopy	retro_nleu_1971,
Oryctolagus cuniculus	ENSOCUG00000015201	1 retrocopy	retro_ocun_443,
Pongo abelii	ENSPPYG00000020820	1 retrocopy	retro_pabe_3133,
Pan troglodytes	ENSPTRG00000022372	1 retrocopy	retro_ptro_2521,
Rattus norvegicus	ENSRNOG00000049744	1 retrocopy	retro_rnor_2843,
Ictidomys tridecemlineatus	ENSSTOG00000011179	1 retrocopy	retro_itri_500,