RetrogeneDB ID: retro_cjac_4165

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:52907015..52907368(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000015775
• Aliases: None
• Description: None

Sequence

>retro_cjac_4165
ATGGAGCATCCACAGCCCCATGAGGAAAAGGCAGGTTGTCTGCTTTTTGCCAAGATGACGGGCTACTCACACTGGCTAGC
CTGGATTGACGAATTCCCAGAGAGAACTATGAAGTCTCCAAGAAAAAAAGCATTCTATTTTTTTCTTTCGGCACCCATGA
CTGCATTTCTAGTTTCCAAAGACCTTTTCCCATATGAGGACTACAAAGAGAGTTTAGAAAGTCAAACAAATAGAAAGGAT
TTAGTGAAGGATTGTGGAAAATAGAAAACAACCCAGGAATAAAGTTTACTGGATGCCAGGCAATTCAGCAACAATAATCT
TCAGAAACTGAGGTAGAAGGCACTGCCAGTGCA

Alignment

ORF - retro_cjac_4165 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.03 %
• Parental protein coverage: 58.13 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MARPRPREYKAGDLVFAKMKGYPHWPARIDELPEGAVKPPANKYPIFFFGTHETAFLGPKDLFPYKEYKD
          M..P.P.E.KAG.L.FAKM.GY.HW.A.IDE.PE...K.P..K...FF.....TAFL..KDLFPY..YK.
Retrocopy MEHPQPHEEKAGCLLFAKMTGYSHWLAWIDEFPERTMKSPRKKAFYFFLSAPMTAFLVSKDLFPYEDYKE

Parental  -KFGKSNKRKGFNEGLWEIENNPGVKFTGYQAIQQQSSSETEGEGGNTA
          ..F.KSNK.KGF.EGLW.IENNPG.KFTG.QAIQQQ.SSETE.EG...A
Retrocopy <EFRKSNK*KGFSEGLWKIENNPGIKFTGCQAIQQQ*SSETEVEGTASA

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	5.06 RPM
SRP051959_heart	0.00 RPM	20.70 RPM
SRP051959_kidney	0.00 RPM	5.13 RPM
SRP051959_liver	0.04 RPM	1.34 RPM
SRP051959_lung	0.00 RPM	12.79 RPM
SRP051959_lymph_node	0.00 RPM	2.97 RPM
SRP051959_skeletal_muscle	0.02 RPM	3.14 RPM
SRP051959_spleen	0.00 RPM	6.74 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4165 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4165 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4165 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018527	1 retrocopy	retro_btau_1740,
Callithrix jacchus	ENSCJAG00000006157	2 retrocopies	retro_cjac_338, retro_cjac_4022,
Callithrix jacchus	ENSCJAG00000012471	1 retrocopy	retro_cjac_4069,
Callithrix jacchus	ENSCJAG00000015775	1 retrocopy	retro_cjac_4165 ,
Dasypus novemcinctus	ENSDNOG00000003696	2 retrocopies	retro_dnov_619, retro_dnov_819,
Echinops telfairi	ENSETEG00000010466	1 retrocopy	retro_etel_1234,
Loxodonta africana	ENSLAFG00000002512	1 retrocopy	retro_lafr_676,
Ictidomys tridecemlineatus	ENSSTOG00000028389	2 retrocopies	retro_itri_292, retro_itri_864,
Tursiops truncatus	ENSTTRG00000004950	1 retrocopy	retro_ttru_1471,
Vicugna pacos	ENSVPAG00000004599	1 retrocopy	retro_vpac_380,