RetrogeneDB ID: retro_cjac_2462

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:110501369..110502393(-)
• Located in intron of: ENSCJAG00000005257

Retrocopy information

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

Parental gene information

• Parental gene symbol: OAT
• Ensembl ID: ENSCJAG00000012633
• Aliases: None
• Description: ornithine aminotransferase [Source:HGNC Symbol;Acc:8091]

Sequence

>retro_cjac_2462
CTTATTATACATGGAGTTCATTCTTCAGTGGCTTCTGCTACATCTGTTGCAACTAAAAGAACAGTCCAAGGCCCTCCAAG
TTCTGATTACATTTTTTAAAGAGTATCTAAGTATGGTGCGCACAATTACCATCCTTTACCTGTAGCCCTGGAGAGAGGAA
AAGGCATTTACTTATGGGATGTAGAGGGCAGAAAATATTTTGACTTCCTGAGTTCTTACAGTGCTGTCCACCAAGGTCAT
TGTCACCCCAAGATTGTGAATGCTCTGAAGAGTCAAGCGGACAAATTGACCTTGACATCTAGAGCTTTCTATAATAACGT
ATTTGGTGAATATGAGGAGTATATTACTAAACTTTTCAACTACCACAAAGTTCTTCCTATGAATACAGGAGTGGAGGCTG
GAGAGACTGCCTGTAAACTGGCTCGTAGGTGGAGCTATACTGTGAAGGGCATTCCGAAATACAAAGCAAAGGTTGTTTTT
GCAGCTGGAAACTTTTGGGGTAGGACATTGTCTGCTATCTCCAGTTCCACAGACCCGACCAGTTACGATGGTTTTGGACC
GTTCATGCCAGGATTTGATGTCATTCCCTATAAGGAACTGCCTGCACTGGAGCGTGCTCTTCAGGATCCAAATGTGGCTG
CGTTCATGGTAGAGCCAATTCAGGGTGAAGCAGGCATTGTTGTTCTGGATCCCGGTTACCTGTTGGGAGTGCGAGAGCTC
TGCACCAGGCACCAGGTCCTGTTTATTGCTGATGAAATACAGACAGGATTGGCCAGAACTGGTAGATGGCTGGCTGTTGA
TCATGAAAATGTCAGACCTGATATAGTCCTCCTTGGAAAGGCCCTTTCTGGGGGCTTATACCCGGTGTCTGCGGTGCTGT
GTGATGATGACAATGCTGACCATTAAGCCAGGGGAACATGGGTCCACTTACGGTGGCAACTAACTAGGCCCTCGAGTGGC
TATTGGAGCCCTTGAGATTTTGGAAGAAGAAAACTTTGCTGAAAATGCAGAAAAAATGGATATT

Alignment

ORF - retro_cjac_2462 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.0 %
• Parental protein coverage: 77.9 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VLSRGVHSSVASATSVATKRTVQGPPSSDYIFERESKYGAHNYHPLPVALERGKGIYLWDVEGRKYFDFL
          ....GVHSSVASATSVATKRTVQGPPSSDYIF.R.SKYGAHNYHPLPVALERGKGIYLWDVEGRKYFDFL
Retrocopy LIIHGVHSSVASATSVATKRTVQGPPSSDYIF*RVSKYGAHNYHPLPVALERGKGIYLWDVEGRKYFDFL

Parental  SSYSAVNQGHCHPKIVNALKSQADILTLTSRAFYNNVLGEYEEYITKLFNYHKVLPMNTGVEAGETACKL
          SSYSAV.QGHCHPKIVNALKSQAD.LTLTSRAFYNNV.GEYEEYITKLFNYHKVLPMNTGVEAGETACKL
Retrocopy SSYSAVHQGHCHPKIVNALKSQADKLTLTSRAFYNNVFGEYEEYITKLFNYHKVLPMNTGVEAGETACKL

Parental  ARRWGYTVKGIPKYKAKVVFAAGNFWGRTLSAISSSTDPTSYDGFGPFMPGFDVIPYNDLPALERALQDP
          ARRW.YTVKGIPKYKAKVVFAAGNFWGRTLSAISSSTDPTSYDGFGPFMPGFDVIPY..LPALERALQDP
Retrocopy ARRWSYTVKGIPKYKAKVVFAAGNFWGRTLSAISSSTDPTSYDGFGPFMPGFDVIPYKELPALERALQDP

Parental  NVAAFMVEPIQGEAGVVVPDPGYLLGVRELCTRHQVLFIADEIQTGLARTGRWLAVDHENVRPDIVLLGK
          NVAAFMVEPIQGEAG.VV.DPGYLLGVRELCTRHQVLFIADEIQTGLARTGRWLAVDHENVRPDIVLLGK
Retrocopy NVAAFMVEPIQGEAGIVVLDPGYLLGVRELCTRHQVLFIADEIQTGLARTGRWLAVDHENVRPDIVLLGK

Parental  ALSGGLYPVSAVLCDDD-IMLTIKPGEHGSTYGGNPLGSRVAIAALEVLEEENLAENAEKLGI
          ALSGGLYPVSAVLC.DD..MLTIKPGEHGSTYGGN.LG.RVAI.ALE.LEEEN.AENAEK..I
Retrocopy ALSGGLYPVSAVLC-DD>TMLTIKPGEHGSTYGGN*LGPRVAIGALEILEEENFAENAEKMDI

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	0.09 RPM	102.73 RPM
SRP051959_heart	0.07 RPM	55.32 RPM
SRP051959_kidney	0.16 RPM	134.51 RPM
SRP051959_liver	0.04 RPM	25.58 RPM
SRP051959_lung	0.08 RPM	66.94 RPM
SRP051959_lymph_node	0.00 RPM	26.67 RPM
SRP051959_skeletal_muscle	0.07 RPM	32.74 RPM
SRP051959_spleen	0.00 RPM	38.09 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2462 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2462 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2462 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012633	1 retrocopy	retro_cjac_2462 ,
Homo sapiens	ENSG00000065154	1 retrocopy	retro_hsap_4828,
Gorilla gorilla	ENSGGOG00000000848	1 retrocopy	retro_ggor_3010,
Macropus eugenii	ENSMEUG00000005655	1 retrocopy	retro_meug_613,
Mus musculus	ENSMUSG00000030934	1 retrocopy	retro_mmus_3475,
Nomascus leucogenys	ENSNLEG00000000482	2 retrocopies	retro_nleu_2176, retro_nleu_503,
Pongo abelii	ENSPPYG00000002737	2 retrocopies	retro_pabe_2989, retro_pabe_3754,
Pan troglodytes	ENSPTRG00000003028	1 retrocopy	retro_ptro_3213,
Sus scrofa	ENSSSCG00000010734	1 retrocopy	retro_sscr_1181,
Tursiops truncatus	ENSTTRG00000004225	1 retrocopy	retro_ttru_87,