RetrogeneDB ID: retro_cjac_780

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 10:44480521..44481267(-)
• Located in intron of: ENSCJAG00000010005

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNC
• Ensembl ID: ENSCJAG00000001388
• Aliases: None
• Description: cyclin C [Source:HGNC Symbol;Acc:1581]

Sequence

>retro_cjac_780
ATGGCAGGGAACTTTTGGCAGAGCTCCTACTATTTGCAATGGATTTTGGATAAACAAGATCTGTTGAAGGAGAGCCAAAA
GGATTTAAAGTCTCTCTCAGAAGAAGAATATTGGAAGTTACAAATATTTTTTACAAATGTTATCTAAACATTGGGTGAAC
ATCTTAAATGAAGACAACAAGTTATTGCCACTGCTATGGTATATTTCCAAGAGATTCTATACCAGGTATTCTCTGAAAAG
TATAGAGCCTGTATTAATAGCTCCTACATGTGTGTTTTTGGCATCCAAAGTTGAGGAATTTGGAATCTTTTCAAATACAA
GATTGACTGCTGCTGCTACTTCTGTATTAAAAACTAGATTTTCATATGCCTTTCCAAAGAAGTTGCCTTATAGGATGAAT
CCTATATTAGAATGTGAATTCCACCTGTTAGAACTAAAGGATTGTTGCTTGATAGTGTATCATCCTTAGTCCTTTGCTCC
AGCATGTGCAGGACGTGGGCCAAGAAGACATGTTGCTTCCCCTTGCATGGAGGATAGTGCATGATACCTACAGAGTGCAT
CTCTGCCTACTGTATCGTCCTTTCATGATAGCTTTAGCTTGCCTACATGTAGCCTGTGTTGTACAGCAGAAAGATGCCAG
GCAATGGTTTGCTGAGCTTTCTGTGGATATGGAAAAGATTTTGGAAATAATCAGGGTTATTTTAAAACTATATGAATAGT
GGAAGAATTTCGATGAAAGAAGAGAT

Alignment

ORF - retro_cjac_780 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.26 %
• Parental protein coverage: 87.99 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAGNFWQSSHYLQWILDKQDLLKERQKDLKFLSEEEYWKLQIFFTNVIQALGEHLKLRQQVIATATVYF-
          MAGNFWQSS.YLQWILDKQDLLKE.QKDLK.LSEEEYWKLQIFFTNVI..LGEHLK.RQQVIATA.VYF.
Retrocopy MAGNFWQSSYYLQWILDKQDLLKESQKDLKSLSEEEYWKLQIFFTNVI*TLGEHLK*RQQVIATAMVYF>

Parental  KRFYARYSLKSIDPVLMAPTCVFLASKVEEFGVVSNTRLTAAATSVLKTRFSYAFPKEFPYRMNHILECE
          KRFY.RYSLKSI.PVL.APTCVFLASKVEEFG..SNTRLTAAATSVLKTRFSYAFPK..PYRMN.ILECE
Retrocopy KRFYTRYSLKSIEPVLIAPTCVFLASKVEEFGIFSNTRLTAAATSVLKTRFSYAFPKKLPYRMNPILECE

Parental  FYLLELMDCCLIVYHP-YRPLLQYVQDMGQEDMLLPLAWRIVNDTYRTDLCLLYPPFMIALACLHVACVV
          F.LLEL.D.C.........PLLQ.VQD.GQEDMLLPLAWRIV.DTYR..LCLLY.PFMIALACLHVACVV
Retrocopy FHLLELKD-CCLIVYH>LSPLLQHVQDVGQEDMLLPLAWRIVHDTYRVHLCLLYRPFMIALACLHVACVV

Parental  QQKDARQWFAELSVDMEKILEIIRVILKLYEQWKNFDERKE
          QQKDARQWFAELSVDMEKILEIIRVILKLYE.WKNFDER..
Retrocopy QQKDARQWFAELSVDMEKILEIIRVILKLYE*WKNFDERRD

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	18.55 RPM
SRP051959_heart	0.02 RPM	16.10 RPM
SRP051959_kidney	0.00 RPM	23.83 RPM
SRP051959_liver	0.00 RPM	24.61 RPM
SRP051959_lung	0.00 RPM	19.29 RPM
SRP051959_lymph_node	0.02 RPM	21.39 RPM
SRP051959_skeletal_muscle	0.02 RPM	10.70 RPM
SRP051959_spleen	0.00 RPM	22.63 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_780 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_780 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_780 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015744	3 retrocopies	retro_btau_1206, retro_btau_1536, retro_btau_1836,
Callithrix jacchus	ENSCJAG00000001388	1 retrocopy	retro_cjac_780 ,
Callithrix jacchus	ENSCJAG00000006738	1 retrocopy	retro_cjac_1273,
Callithrix jacchus	ENSCJAG00000011407	1 retrocopy	retro_cjac_1814,
Dasypus novemcinctus	ENSDNOG00000011999	3 retrocopies	retro_dnov_1153, retro_dnov_216, retro_dnov_2243,
Echinops telfairi	ENSETEG00000002643	1 retrocopy	retro_etel_1441,
Otolemur garnettii	ENSOGAG00000001116	1 retrocopy	retro_ogar_2123,
Sorex araneus	ENSSARG00000004726	2 retrocopies	retro_sara_141, retro_sara_583,