RetrogeneDB ID: retro_cjac_952

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 12:2011491..2011893(+)
• Located in intron of: ENSCJAG00000014784

Retrocopy information

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

Parental gene information

• Parental gene symbol: C2orf68
• Ensembl ID: ENSCJAG00000019632
• Aliases: None
• Description: chromosome 2 open reading frame 68 [Source:HGNC Symbol;Acc:34353]

Sequence

>retro_cjac_952
GTGCACCATATCTGACGGAACCAGATTGCCCGGGACGACTACGACAAGAAGGTGAAGCAGGCGGCCAAGGAGGTGAGGAG
GTGGCACACGCCCGCGCCTACGTGGCCCTGCAAGCCAGACCTGCAGGTGTACCTGCCACGACACCGAGCTGTCTCTGCCC
ACCCATGCAACCCAGACTATGAAGAATCCAGTGAAAGCAGCAGTAGTGGAGGCTCCGAGTTGGAGCCTTCTGGCCATCAG
CTTTTCTGCTTAGAGTACGAGGCAGACAGTGGAGAGGTCACATCAGTTATCGTGTATCAGGGCGATGACCCGGGAAGGGT
GAGTGAGGAGGTGTCAGCAGGCGCGCCTCTGGATCCGCCGATGCGAGAAGCGCTCCAGGAGGAGACTGCAAGGCGCCAGA
GC

Alignment

ORF - retro_cjac_952 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.49 %
• Parental protein coverage: 83.73 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VHHIRRNQIARDDYDKKVKQAAKEKVRRRHTPAPTRPRKPDLQVYLPRHRDVSAHPRNPDYEESSESSSS
          VHHI.RNQIARDDYDKKVKQAAKE.VRR.HTPAPT.P.KPDLQVYLPRHR.VSAHP.NPDYEESSESSSS
Retrocopy VHHI*RNQIARDDYDKKVKQAAKE-VRRWHTPAPTWPCKPDLQVYLPRHRAVSAHPCNPDYEESSESSSS

Parental  GGSELEPSGHQLFCLEYEADSGDVTSVIVYQGDDPGRVSEEVSARTPLDPPMREALKLRIQEEIAKRQS
          GGSELEPSGHQLFCLEYEADSG.VTSVIVYQGDDPGRVSEEVSA..PLDPPMREAL....QEE.A.RQS
Retrocopy GGSELEPSGHQLFCLEYEADSGEVTSVIVYQGDDPGRVSEEVSAGAPLDPPMREAL----QEETARRQS

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	0.11 RPM	3.33 RPM
SRP051959_heart	0.18 RPM	2.82 RPM
SRP051959_kidney	0.18 RPM	4.10 RPM
SRP051959_liver	0.09 RPM	2.56 RPM
SRP051959_lung	0.55 RPM	6.83 RPM
SRP051959_lymph_node	0.59 RPM	7.58 RPM
SRP051959_skeletal_muscle	0.04 RPM	2.18 RPM
SRP051959_spleen	0.23 RPM	4.96 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_952 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_952 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_952 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019632	4 retrocopies	retro_cjac_2584, retro_cjac_2787, retro_cjac_453, retro_cjac_952 ,
Equus caballus	ENSECAG00000014919	1 retrocopy	retro_ecab_479,
Otolemur garnettii	ENSOGAG00000033817	1 retrocopy	retro_ogar_1736,