RetrogeneDB ID: retro_cjac_2025

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 21:18875107..18876003(+)
• Located in intron of: ENSCJAG00000003218

Retrocopy information

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

Parental gene information

• Parental gene symbol: AGPAT4
• Ensembl ID: ENSCJAG00000012323
• Aliases: None
• Description: 1-acylglycerol-3-phosphate O-acyltransferase 4 [Source:HGNC Symbol;Acc:20885]

Sequence

>retro_cjac_2025
ATGCAGCTCTTCACTCTCCTTTGGCCAATTAACAAGCAGCTCTTCAGGAAGATCAACTGCAGACTGTCCTATTGCATCTC
AAGCCAGCTGGTGATGCTGCTGGAGTGGTGGTCGGACATGGAATGCACCATCTTCATGGACCCGCGAGCCTACCCCAAGT
ATGGGAAGGAAAATGCCATCGTGATTCTCAACCACAAGTTTGAAATTGACTTTCTCTGTGGCTGGAGCCTGTCCCAACGC
TTTGGGCTCTTAGGGGGTCCAAGGTCCTGGCCAAGAAAGAGCTGGCCTACGTCCCGATCATCGGCTGGATGTGGTACTTC
ACCAAGATGGTCTTCTGCACGCGCAAGTGGGAGCAGGATCGCAAGACAGTTGCCACCAGCCTACAGCACCTCCGGGACTA
CCCCGAGAAATATTTTTTCCTGATCCACTGTGAGGGCACACGGTTCACAGAGAAGCAGCACGAGATCAGCATGCAGGTGG
CCCGGGCCAAGGGGCTGCCTAGCCTCAAGCACCACCGGTTGCCGTGAACCAAGGGCTTCGCCATCACTGTGAGGAGCTTG
AGAAATGTAGTTTCAGCTGTATATGACTGTACACTCAATTTCAGAAATAATGAAAATCCAACACTGCTGGGAGTCCTAAA
CGGAAAGAAATATCATGCAGATTTGTATGTTAGGAGGATTCCACTGGAAGACATCCCTGAAGACGATGCCAAGTGCTCGG
CCTGGCTGCACAAACTCTACCAGGAGAAGGATGCATTTCAGGAGGAGTACTACAGGATGGGCACCTTCCCGGAGACGCCT
ATGGTGCCCCCCAGGCGGCCCTGGACCCTAGTGAACTGGCTGTTTTGGGCCTTATTGGTGTTCTACCCTTTCTTCCAGTT
CTTGGTCAGCAGTATC

Alignment

ORF - retro_cjac_2025 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.68 %
• Parental protein coverage: 86.21 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MQLFTLLLWPINKQLFRKINCRLSYCISSQLVMLLEWWSGTECTIFTDPRAYPKYGKENAIVVLNHKFEI
          MQLFTLL.WPINKQLFRKINCRLSYCISSQLVMLLEWWS..ECTIF.DPRAYPKYGKENAIV.LNHKFEI
Retrocopy MQLFTLL-WPINKQLFRKINCRLSYCISSQLVMLLEWWSDMECTIFMDPRAYPKYGKENAIVILNHKFEI

Parental  DFLCGWSLSERFGLLGG-SKVLAKKELAYVPIIGWMWYFTEMVFCTRKWEQDRKTVATSLQHLRDYPEKY
          DFLCGWSLS.RFGLLGG.SKVLAKKELAYVPIIGWMWYFT.MVFCTRKWEQDRKTVATSLQHLRDYPEKY
Retrocopy DFLCGWSLSQRFGLLGG<SKVLAKKELAYVPIIGWMWYFTKMVFCTRKWEQDRKTVATSLQHLRDYPEKY

Parental  FFLIHCEGTRFTEKKHEISMQVARAKGLPSLKHHLLPRTKGFAITVRSLRNVVSAVYDCTLNFRNNENPT
          FFLIHCEGTRFTEK.HEISMQVARAKGLPSLKHH.LP.TKGFAITVRSLRNVVSAVYDCTLNFRNNENPT
Retrocopy FFLIHCEGTRFTEKQHEISMQVARAKGLPSLKHHRLP*TKGFAITVRSLRNVVSAVYDCTLNFRNNENPT

Parental  LLGVLNGKKYHADLYVRRIPLEDIPEDDAKCSAWLHKLYQEKDAFQEEYYRTGTFPETPMVPPRRPWTLV
          LLGVLNGKKYHADLYVRRIPLEDIPEDDAKCSAWLHKLYQEKDAFQEEYYR.GTFPETPMVPPRRPWTLV
Retrocopy LLGVLNGKKYHADLYVRRIPLEDIPEDDAKCSAWLHKLYQEKDAFQEEYYRMGTFPETPMVPPRRPWTLV

Parental  NWLFWASLMLYPFFQFLVSMI
          NWLFWA.L..YPFFQFLVS.I
Retrocopy NWLFWALLVFYPFFQFLVSSI

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	9.01 RPM
SRP051959_heart	0.00 RPM	2.56 RPM
SRP051959_kidney	0.29 RPM	18.77 RPM
SRP051959_liver	0.00 RPM	0.52 RPM
SRP051959_lung	0.03 RPM	1.63 RPM
SRP051959_lymph_node	0.00 RPM	1.26 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.85 RPM
SRP051959_spleen	0.00 RPM	1.13 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2025 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2025 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2025 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	ENSCJAG00000012323	1 retrocopy	retro_cjac_2025 ,