RetrogeneDB ID: retro_cjac_259

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 17:38384566..38384929(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000023360
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000034456
• Aliases: None
• Description: None

Sequence

>retro_cjac_259
ATGGCGGAGCCCTCGTGCGCCCGACGCCCGGTGCCTCTCATCGAGTCGGAGCTATACTGCCTTATCGCCCGGTACCTATC
CGCGGGCCCGTGTCGGACAGCGGCCCAGGTGCTGGTGCAGGAGCTGGAGCAGTACCAATTGTTGCCAAAGAGGTCGGACT
GGGAGGGCAATGAGCACAACAGGAGCTACGAGGAATTGGTCTTGTCCAATAAGCATGTGGCTCCTGATCATCTGTTGCAA
ATCTGCCAACGCATGGGTCCTATGTTGGTTAAAGAAATTCCACCCAGTATTTCAAGAGTCACTTCTTTACTTGGTGCAGG
AAGGCAATCTTTGCTACATACAGCAAAAGATACCTTCATTTGA

Alignment

ORF - retro_cjac_259 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.26 %
• Parental protein coverage: 67.95 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PPSSPELYYLIARFLQSGPCNKSAQVLVQELEEHQLIPRRLDWEGKEHRRSFEDLVAANAHIPPDYLLKI
          P....ELY.LIAR.L..GPC...AQVLVQELE..QL.P.R.DWEG.EH.RS.E.LV..N.H..PD.LL.I
Retrocopy PLIESELYCLIARYLSAGPCRTAAQVLVQELEQYQLLPKRSDWEGNEHNRSYEELVLSNKHVAPDHLLQI

Parental  CERIGPLLDKEIPQSVPGVQTLLGVGRQSLLRDAKD
          C.R.GP.L.KEIP.S...V..LLG.GRQSLL..AKD
Retrocopy CQRMGPMLVKEIPPSISRVTSLLGAGRQSLLHTAKD

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	0.18 RPM	2.57 RPM
SRP051959_heart	0.14 RPM	1.05 RPM
SRP051959_kidney	0.09 RPM	1.64 RPM
SRP051959_liver	0.13 RPM	1.06 RPM
SRP051959_lung	0.11 RPM	2.29 RPM
SRP051959_lymph_node	0.18 RPM	2.51 RPM
SRP051959_skeletal_muscle	0.09 RPM	0.52 RPM
SRP051959_spleen	0.15 RPM	1.95 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_259 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_259 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_259 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000034456	1 retrocopy	retro_cjac_259 ,
Nomascus leucogenys	ENSNLEG00000002210	1 retrocopy	retro_nleu_2626,