RetrogeneDB ID: retro_cjac_155

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 8:97016118..97016523(+)
• Located in intron of: ENSCJAG00000010260

Retrocopy information

• Ensembl ID: ENSCJAG00000021991
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000008767
• Aliases: None
• Description: None

Sequence

>retro_cjac_155
ATGGGCGCCATGTGCCTTCCGCACACCTCGCTGTCCGAGTATGTACTGCTCTTAGGCACCGCCCTGGGCTCCCATGGCCA
CTCCGGGTGCTACTGGGCTAAGATCTCCGATACCATCATCTCTGTCACCTTCCACCAGTGGAGAGAGGGCACCACCAAAA
GTGAGGTCTTCTACCCAGGAGTGACGGTAGTGCATGGGCCTGGTGAAGCCACAGCTGTGGAGTGGGGGCCAAACACATGG
ATGGTGGAGTACGGCCAGGGTGTCATCCCATCCACCCTGGCCTTCGTTCTGGCTGACACTGTCTTCAGCACCCAGGACTT
CCTCACCCTCTTCTATACTCTTCGCTCCTATGCCCGGGGCCTCTGGCTTGAGCTCACCATCTACCTCTTTGGCCAGGACC
CTTGA

Alignment

ORF - retro_cjac_155 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.04 %
• Parental protein coverage: 60.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGAMCLLHASLSEYVLLFGTALGSRGHSGRYWAEISDTIISGTFHQWREGTTKSEVFYPGETVVHGPGEA
          MGAMCL.H.SLSEYVLL.GTALGS.GHSG.YWA.ISDTIIS.TFHQWREGTTKSEVFYPG.TVVHGPGEA
Retrocopy MGAMCLPHTSLSEYVLLLGTALGSHGHSGCYWAKISDTIISVTFHQWREGTTKSEVFYPGVTVVHGPGEA

Parental  TAVEWGPNTWMVEYGRGVIPSTLAFALADTVFSTQDFLTLFYTLRSYARGLRLELTTYLFGQDP
          TAVEWGPNTWMVEYG.GVIPSTLAF.LADTVFSTQDFLTLFYTLRSYARGL.LELT.YLFGQDP
Retrocopy TAVEWGPNTWMVEYGQGVIPSTLAFVLADTVFSTQDFLTLFYTLRSYARGLWLELTIYLFGQDP

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	0.24 RPM	6.10 RPM
SRP051959_heart	0.25 RPM	5.42 RPM
SRP051959_kidney	0.20 RPM	8.65 RPM
SRP051959_liver	0.24 RPM	17.59 RPM
SRP051959_lung	0.16 RPM	5.84 RPM
SRP051959_lymph_node	0.62 RPM	6.62 RPM
SRP051959_skeletal_muscle	0.20 RPM	2.73 RPM
SRP051959_spleen	0.29 RPM	7.27 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_155 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_155 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_155 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008767	1 retrocopy	retro_cjac_155 ,
Microcebus murinus	ENSMICG00000002386	1 retrocopy	retro_mmur_119,
Ochotona princeps	ENSOPRG00000009222	1 retrocopy	retro_opri_691,