RetrogeneDB ID: retro_cjac_2764

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:124194236..124194641(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000003896
• Aliases: None
• Description: Glutathione peroxidase [Source:UniProtKB/TrEMBL;Acc:F6T6G6]

Sequence

>retro_cjac_2764
GTGAACGAACTGCAGCGGCGCCTCGGGCTCCGGGGCCTGGTGGTGCTCGGCTTCCCGTGCAACCGGTTTGGACATCAGGA
GAACGCCAAGAACGAAGAGATTTTGAATTCCCTCAAGTACGTCCGACCTGGTGGTGGGTTCGAGCCCAACTTCATGCTCT
TCGAGAAGTGCGAGGTGAACGGTGAGGGGTCGCACCCTCTCTTGGCCTTCCTGCGGGAGGCCCTGCCAGCGCCCAGCAAC
AACGCCTCTGAGCTCATGACCGACCCCAAGCTCATCACCTGGTCTCCGGTATGCCGAAACGATGTTGCATGGAACTTTGA
GAAGTTCCTCGTGGGCCCTGACGGTGTTCCTGTGCGCTGGTACAGCCACCGCTTCCAGACCATTGACATCAAGCCTGACA
TCGAA

Alignment

ORF - retro_cjac_2764 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.63 %
• Parental protein coverage: 93.1 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNELQRRLGPRGLVVLGFPCNQFGHQENAKNEEILNSLKYVRPGGGFEPNFMLFEKCEVNSAGSHPLFAF
          .NELQRRLG.RGLVVLGFPCN.FGHQENAKNEEILNSLKYVRPGGGFEPNFMLFEKCEVN..GSHPL.AF
Retrocopy VNELQRRLGLRGLVVLGFPCNRFGHQENAKNEEILNSLKYVRPGGGFEPNFMLFEKCEVNGEGSHPLLAF

Parental  LREALPAPSDDATALMTDPKLITWSPVCRNDVAWNFEKFLVGPDGIPVRRYSRRFQTIDIEPDIE
          LREALPAPS..A..LMTDPKLITWSPVCRNDVAWNFEKFLVGPDG.PVR.YS.RFQTIDI.PDIE
Retrocopy LREALPAPSNNASELMTDPKLITWSPVCRNDVAWNFEKFLVGPDGVPVRWYSHRFQTIDIKPDIE

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	18.88 RPM
SRP051959_heart	0.00 RPM	18.19 RPM
SRP051959_kidney	0.02 RPM	27.11 RPM
SRP051959_liver	0.00 RPM	33.79 RPM
SRP051959_lung	0.00 RPM	11.63 RPM
SRP051959_lymph_node	0.00 RPM	11.67 RPM
SRP051959_skeletal_muscle	0.00 RPM	14.00 RPM
SRP051959_spleen	0.00 RPM	16.30 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2764 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2764 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2764 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003896	6 retrocopies	retro_cjac_217, retro_cjac_2588, retro_cjac_2764 , retro_cjac_3464, retro_cjac_447, retro_cjac_448,