RetrogeneDB ID: retro_cjac_4059

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:45715980..45716546(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFS3
• Ensembl ID: ENSCJAG00000020194
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) Fe-S protein 3, 30kDa (NADH-coenzyme Q reductase) [Source:HGNC Symbol;Acc:7710]

Sequence

>retro_cjac_4059
ATTCAGGTGTCCTTCTTCAATGAGTTATAGATCTGTATCCATCCTGATGGCGTCATCCCAGCGCTGACTTTCCTCAAGGA
TCATACCAATGTACAGTTCAAAACCCTGGCTGACTTGACAGCACTGAACATCCCGACTCAGCAGAACCATTTTGAGATTG
TCTACAACCTGTTGTCTCTGTGCTTCAACTCACGGATCCATGTGAAGATCTACACAGATGAGCTGACGCCCATTCAGTCC
ATTATATCTGTGTTCAAGGAAGCCAACTGGTATGAGAGGGAGATCTGGGACATGTTTGGAGTCTTCTTTGCTAACCACCC
AGATCTAAGAAGGATCCTGACAGGTTATGGCTTCGAGGGGCATCCTTTCCAGAAAGACTTCCCTCTATCTGGCTATGTCG
AGTTATGCTATGATGAAGAGGGGAAGCAGTGGTGGCAGAGCCAGTGGAGTTGGCCCAAGAGTTCCGCAAATTTGACCTCA
ACAGCCCCTAGGAGGCTTTCCCAACCTATCGCCAACCCCCAGAGAGTATCAAGCTTGAAGCCAGAGAAAAGAAGCCTGAA
GCCAAG

Alignment

ORF - retro_cjac_4059 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.16 %
• Parental protein coverage: 72.14 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VQVSLFDELEICIHPDGIIPVLTFLKDHTNAQFKSLADLTAVDIPTRQNRFEIVYNLLSLRFNSRIRVKT
          .QVS.F.EL.ICIHPDG.IP.LTFLKDHTN.QFK.LADLTA..IPT.QN.FEIVYNLLSL.FNSRI.VK.
Retrocopy IQVSFFNEL*ICIHPDGVIPALTFLKDHTNVQFKTLADLTALNIPTQQNHFEIVYNLLSLCFNSRIHVKI

Parental  YTDELTPIESLTSVFKAANWYEREVWDMFGVFFVNHPDLRRILTDYGFEGHPFRKDFPLSGYVELRYDDE
          YTDELTPI.S..SVFK.ANWYERE.WDMFGVFF.NHPDLRRILT.YGFEGHPF.KDFPLSGYVEL.YD.E
Retrocopy YTDELTPIQSIISVFKEANWYEREIWDMFGVFFANHPDLRRILTGYGFEGHPFQKDFPLSGYVELCYDEE

Parental  VKR-VVAEPVELAQEFRKFDLNSPWEAFPIYRQPPESLKLEAGEKKPEAK
          .K..VVAEPVELAQEFRKFDLNSP.EAFP.YRQPPES.KLEA.EKKPEAK
Retrocopy GKQ<VVAEPVELAQEFRKFDLNSP*EAFPTYRQPPESIKLEAREKKPEAK

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	21.26 RPM
SRP051959_heart	0.00 RPM	37.52 RPM
SRP051959_kidney	0.00 RPM	29.06 RPM
SRP051959_liver	0.00 RPM	34.87 RPM
SRP051959_lung	0.00 RPM	14.66 RPM
SRP051959_lymph_node	0.00 RPM	15.36 RPM
SRP051959_skeletal_muscle	0.00 RPM	59.57 RPM
SRP051959_spleen	0.00 RPM	16.64 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4059 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4059 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4059 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008411	1 retrocopy	retro_cfam_1052,
Callithrix jacchus	ENSCJAG00000020194	1 retrocopy	retro_cjac_4059 ,
Equus caballus	ENSECAG00000013454	1 retrocopy	retro_ecab_431,
Erinaceus europaeus	ENSEEUG00000007356	1 retrocopy	retro_eeur_52,
Mus musculus	ENSMUSG00000005510	2 retrocopies	retro_mmus_2338, retro_mmus_792,