RetrogeneDB ID: retro_cjac_569

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:82181105..82181712(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000002901
• Aliases: None
• Description: None

Sequence

>retro_cjac_569
GTGTCCCCCAATGCCAGCCCCAAGATGGGCCGGCACGCGGGGTCTGCTGAGCTGTACTGCACTTCTGACATCTACGAGGC
AGTGTCGGGAGACGCGTGGTGGTAGCGCTCGCTGCTGTGGAGCCTGCTGAGTTGGATTTCGGAGAGGGCGAGGGCACCAC
CTGCAGCACATCAGCGACCGCGAGATGCCCGAAAATTTAGCTTTGGAGTCGAACCCTTCTGACCATCCAAGGGCAAGCAC
AATTTTCCTGAGCAAATCTCAAACAGATGTGCGAGAAAAGAGGAAGAGCAACCATTTAAACCATGTATCCAGGGCAGCTT
ACTAAAAAGTATAGCTCATGCTCAACAATATTTCTAGATGACAGCACAGTCAGCCAGCCTAATCTTAGAACCACAGTAAA
ATGTGTGACCTTAGCAATATATTACCACATAAAGAACAGAGATGCAAATAATCCCTGGATATTTTTGATGAGAGATCACA
TCCACTTACACGAGAAGAAGTTCCAGAGAAATACTTTAAGCATGATCCTGAGCACAGATTTATTTACAGATTTGTTCGTA
CTCTTTTTAGTGCTGCACAGATAAAAGCTGAATGTGCAACAGGAACT

Alignment

ORF - retro_cjac_569 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.0 %
• Parental protein coverage: 56.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  VSPNASPKLGRRAGSAELYCASDIYEAASGDA-VAVAPAAVEPAELDFGEGEG-HHLQHISDREMPEDLA
          VSPNASPK.GR.AGSAELYC.SDIYEA.SGDA.V.VA.AAVEPAELDFGEGEG.HHLQHISDREMPE.LA
Retrocopy VSPNASPKMGRHAGSAELYCTSDIYEAVSGDA<VVVALAAVEPAELDFGEGEG<HHLQHISDREMPENLA

Parental  LESNPSDHPRASTIFLSKSQTDVREKRKSNHLNHVS-PGQLTK-KYSSCSTIFLDDSTVSQPNLRTTVKC
          LESNPSDHPRASTIFLSKSQTDVREKRKSNHLNHVS..G.L.K.KYSSCSTIFLDDSTVSQPNLRTTVKC
Retrocopy LESNPSDHPRASTIFLSKSQTDVREKRKSNHLNHVS<QGSLLK<KYSSCSTIFLDDSTVSQPNLRTTVKC

Parental  VTLAIYYHIKNRDANR-SLDIFDERSHPLTREKVPEEYFKHDPEHKFIYRFVRTLFSAAQLTAECAIVT
          VTLAIYYHIKNRDAN..SLDIFDERSHPLTRE.VPE.YFKHDPEH.FIYRFVRTLFSAAQ..AECA..T
Retrocopy VTLAIYYHIKNRDANN<SLDIFDERSHPLTREEVPEKYFKHDPEHRFIYRFVRTLFSAAQIKAECATGT

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	16.84 RPM
SRP051959_heart	0.00 RPM	5.46 RPM
SRP051959_kidney	0.04 RPM	6.99 RPM
SRP051959_liver	0.00 RPM	4.68 RPM
SRP051959_lung	0.00 RPM	6.54 RPM
SRP051959_lymph_node	0.02 RPM	7.33 RPM
SRP051959_skeletal_muscle	0.00 RPM	4.30 RPM
SRP051959_spleen	0.02 RPM	9.39 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_569 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_569 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_569 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001008	1 retrocopy	retro_cjac_3555,
Callithrix jacchus	ENSCJAG00000002901	1 retrocopy	retro_cjac_569 ,
Callithrix jacchus	ENSCJAG00000011445	1 retrocopy	retro_cjac_1164,
Callithrix jacchus	ENSCJAG00000034702	1 retrocopy	retro_cjac_610,
Homo sapiens	ENSG00000163249	3 retrocopies	retro_hsap_1629, retro_hsap_1984, retro_hsap_4845,
Macaca mulatta	ENSMMUG00000020211	1 retrocopy	retro_mmul_2587,
Mus musculus	ENSMUSG00000070871	1 retrocopy	retro_mmus_3072,
Nomascus leucogenys	ENSNLEG00000007131	3 retrocopies	retro_nleu_1164, retro_nleu_2902, retro_nleu_430,
Pongo abelii	ENSPPYG00000013118	3 retrocopies	retro_pabe_1345, retro_pabe_3766, retro_pabe_76,