RetrogeneDB ID: retro_cjac_2103

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 22:20332876..20333482(-)
• Located in intron of: ENSCJAG00000032315

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBFOX2
• Ensembl ID: ENSCJAG00000019456
• Aliases: None
• Description: RNA binding protein, fox-1 homolog (C. elegans) 2 [Source:HGNC Symbol;Acc:9906]

Sequence

>retro_cjac_2103
ATGGAGAAAAAGAAAATGGTAACTCAGGGTAACCAGGAGCCAACAACAACTCCTGACGCGATGGTTCAGCCTTTTACTAC
CATCCCATTTCCACCACCTCCGCAGAATGGAATTCCCACAGAATATGGGGTGCCACACACTCAAGACTATGCCGGCCAGA
CCGGTGAGCATGACCTGACACTCTATGGAAGTACGCAAGCCCATGGGGAGCAGAGCAGCAACTCACCCAGCACACAAAAT
GGATCTCTTACGACAGAAGGTGGAGCACAGACGGATGGCCAGCAGTCACAGACACAAAGTAGTGAAAATTCAGAGAGTAA
ATCTACCCCGAAACGGCTGCATGTCTCTAATATTCCTTTCCGCTTCCGGGACCCTGACCTCCGGCAGATGTTTGGGCAGT
TTGGCAAAATCCTAGATGTAGAAATAATCTTTAATGAACGAGGCTCTAAGGGATTCGGGTTCGTAACTTTCGAGAATAGT
GCTGATGCAGACAGGGCCAGGGAGAAATTACACGGCACCGTGGTAGAGGGCCGTAAAATCGAGGTAAATAATGCTACAGC
ACGTGTAATGACCAATAAGAAGATGGTCACGCCATATGCAAATGGT

Alignment

ORF - retro_cjac_2103 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100. %
• Parental protein coverage: 53.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEKKKMVTQGNQEPTTTPDAMVQPFTTIPFPPPPQNGIPTEYGVPHTQDYAGQTGEHDLTLYGSTQAHGE
          MEKKKMVTQGNQEPTTTPDAMVQPFTTIPFPPPPQNGIPTEYGVPHTQDYAGQTGEHDLTLYGSTQAHGE
Retrocopy MEKKKMVTQGNQEPTTTPDAMVQPFTTIPFPPPPQNGIPTEYGVPHTQDYAGQTGEHDLTLYGSTQAHGE

Parental  QSSNSPSTQNGSLTTEGGAQTDGQQSQTQSSENSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDV
          QSSNSPSTQNGSLTTEGGAQTDGQQSQTQSSENSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDV
Retrocopy QSSNSPSTQNGSLTTEGGAQTDGQQSQTQSSENSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDV

Parental  EIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARVMTNKKMVTPYANG
          EIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARVMTNKKMVTPYANG
Retrocopy EIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARVMTNKKMVTPYANG

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	12.89 RPM
SRP051959_heart	0.12 RPM	27.84 RPM
SRP051959_kidney	0.07 RPM	11.34 RPM
SRP051959_liver	0.04 RPM	12.69 RPM
SRP051959_lung	0.10 RPM	16.14 RPM
SRP051959_lymph_node	0.07 RPM	3.29 RPM
SRP051959_skeletal_muscle	0.13 RPM	34.53 RPM
SRP051959_spleen	0.04 RPM	7.29 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2103 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2103 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2103 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019456	1 retrocopy	retro_cjac_2103 ,