RetrogeneDB ID: retro_cjac_1287

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 14:59610052..59610429(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000010905
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000007852
• Aliases: None
• Description: None

Sequence

>retro_cjac_1287
GGGTACACTCCGGATGAGAAACTGCGGCAGCAGCAGTTGCAAGAGCTGAGAAGGCAATGGATAAAGGACCAGGAGCTGAG
CCCTCGGGAGCTGGTGCTGCCCCCAGAGGCGACGTGGCCTAAGGACAGATTCTGGGATAAGTTTTGGCAAATAAGACCCC
TTGGAGGAATACAGTCTATAAGGTATACCAAAAGAGTATGTTTATTTTTACTTATGTACTTATACGTGCCTGGATTGTTT
ATTATTACGTGAAATATCATGTGGCTACAAAACCATATGGCATCATTCAGTTGAAGCCCAGAATATTCCCAGGTGATACA
GTAGTGGAGACTGGAGAATTAATTCCACCAATGAAAGAATTTCCTGATCAACATCAT

Alignment

ORF - retro_cjac_1287 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.61 %
• Parental protein coverage: 98.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GYTPDEKLRQQQLRALRRQWLKDQELSPREPVLPPEATWPMDRFWDKF-LANKSPWRNMVYKVYRKSMFI
          GYTPDEKLRQQQL..LRRQW.KDQELSPRE.VLPPEATWP.DRFWDKF.LANK.PWRN.VYKVY.KSMFI
Retrocopy GYTPDEKLRQQQLQELRRQWIKDQELSPRELVLPPEATWPKDRFWDKF<LANKTPWRNTVYKVYQKSMFI

Parental  FTCVLIPAWIVHYYVKYHVATKPYAIVQSKPRIFPGDTIVETGEVIPPMKEFPDQHH
          FT.VLI.AWIV.YYVKYHVATKPY.I.Q.KPRIFPGDT.VETGE.IPPMKEFPDQHH
Retrocopy FTYVLIRAWIVYYYVKYHVATKPYGIIQLKPRIFPGDTVVETGELIPPMKEFPDQHH

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	13.25 RPM
SRP051959_heart	0.00 RPM	29.71 RPM
SRP051959_kidney	0.00 RPM	27.09 RPM
SRP051959_liver	0.02 RPM	26.64 RPM
SRP051959_lung	0.00 RPM	7.84 RPM
SRP051959_lymph_node	0.02 RPM	8.06 RPM
SRP051959_skeletal_muscle	0.02 RPM	45.14 RPM
SRP051959_spleen	0.00 RPM	9.47 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1287 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1287 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1287 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000001263	3 retrocopies	retro_acar_110, retro_acar_116, retro_acar_117,
Callithrix jacchus	ENSCJAG00000007852	3 retrocopies	retro_cjac_1287 , retro_cjac_255, retro_cjac_303,
Dasypus novemcinctus	ENSDNOG00000019864	2 retrocopies	retro_dnov_2281, retro_dnov_920,
Ochotona princeps	ENSOPRG00000007428	5 retrocopies	retro_opri_148, retro_opri_525, retro_opri_591, retro_opri_614, retro_opri_722,
Sus scrofa	ENSSSCG00000011003	1 retrocopy	retro_sscr_260,
Tupaia belangeri	ENSTBEG00000013268	2 retrocopies	retro_tbel_195, retro_tbel_197,
Tarsius syrichta	ENSTSYG00000002785	1 retrocopy	retro_tsyr_382,
Tursiops truncatus	ENSTTRG00000012172	1 retrocopy	retro_ttru_1505,