RetrogeneDB ID: retro_cjac_4045

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:20275230..20275752(+)
• Located in intron of: ENSCJAG00000005185

Retrocopy information

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

Parental gene information

• Parental gene symbol: YY1
• Ensembl ID: ENSCJAG00000016853
• Aliases: None
• Description: None

Sequence

>retro_cjac_4045
GTGGGGGAAGGCCGGCCCGATAACTCACCGGATTATTCCGAGTACTTGAAAGGGAAGAAACTTCCTCCCGAGGGATTACC
AGGAATCGATCTCTCAGATCCCAAACAGCTGGCAGAATTTACTAAAATGAAGCCCAAAAGGTCCAAAGACGACCCCCCCA
GAACAGTCCCTTGCGCTCATATTGGCTGCGGAAAGATGTTCAGGGATTATGGCGCCATGAGAAAACATCTCCACATCCAC
GGGCCCAGAGTCCACGTATGTGCAGAATGTGGCAAAGCTTTTATTGAGAGCTCAAAGCTGAAACGACATCAGCTGGTTCA
CACGGGCGAGAAACCCTTTCAGTGCACATTCGAAGGTTGCGGGAAACGCTTTTCCCTTGATTTCAATTTGCGCACACATG
TGCGCATCCACACCGGCGACAAGCCCTTCGTGTGCCCTTTCGATATTTGCAATAGGAAATTCGCCCAGTCAACCAACCTG
AAGACGCATATGTTAACACATGTGAAGAACAAAAGCAGCCAG

Alignment

ORF - retro_cjac_4045 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.43 %
• Parental protein coverage: 63.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IGENSP---PDYSEYMTGKKLPPGGIPGIDLSDPKQLAEFARMKPRKIKEDDAPRTIACPHKGCTKMFRD
          .GE..P...PDYSEY..GKKLPP.G.PGIDLSDPKQLAEF..MKP...K.DD.PRT..C.H.GC.KMFRD
Retrocopy VGEGRPDNSPDYSEYLKGKKLPPEGLPGIDLSDPKQLAEFTKMKPKRSK-DDPPRTVPCAHIGCGKMFRD

Parental  NSAMRKHLHTHGPRVHVCAECGKAFVESSKLKRHQLVHTGEKPFQCTFEGCGKRFSLDFNLRTHVRIHTG
          ..AMRKHLH.HGPRVHVCAECGKAF.ESSKLKRHQLVHTGEKPFQCTFEGCGKRFSLDFNLRTHVRIHTG
Retrocopy YGAMRKHLHIHGPRVHVCAECGKAFIESSKLKRHQLVHTGEKPFQCTFEGCGKRFSLDFNLRTHVRIHTG

Parental  DRPYVCPFDGCNKKFAQSTNLKSHILTHAKAKNNQ
          D.P.VCPFD.CN.KFAQSTNLK.H.LTH.K.K..Q
Retrocopy DKPFVCPFDICNRKFAQSTNLKTHMLTHVKNKSSQ

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	0.35 RPM	11.65 RPM
SRP051959_heart	0.39 RPM	12.38 RPM
SRP051959_kidney	0.42 RPM	13.29 RPM
SRP051959_liver	0.13 RPM	10.94 RPM
SRP051959_lung	0.44 RPM	13.86 RPM
SRP051959_lymph_node	0.59 RPM	13.58 RPM
SRP051959_skeletal_muscle	0.26 RPM	8.58 RPM
SRP051959_spleen	0.27 RPM	13.74 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4045 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4045 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4045 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011146	1 retrocopy	retro_amel_2,
Bos taurus	ENSBTAG00000020819	1 retrocopy	retro_btau_91,
Callithrix jacchus	ENSCJAG00000016853	2 retrocopies	retro_cjac_1931, retro_cjac_4045 ,
Cavia porcellus	ENSCPOG00000020809	2 retrocopies	retro_cpor_1220, retro_cpor_1522,
Equus caballus	ENSECAG00000005805	1 retrocopy	retro_ecab_97,
Homo sapiens	ENSG00000100811	2 retrocopies	retro_hsap_106, retro_hsap_97,
Gorilla gorilla	ENSGGOG00000026332	2 retrocopies	retro_ggor_190, retro_ggor_2,
Mustela putorius furo	ENSMPUG00000002931	1 retrocopy	retro_mputfur_867,
Mus musculus	ENSMUSG00000021264	1 retrocopy	retro_mmus_190,
Nomascus leucogenys	ENSNLEG00000000999	3 retrocopies	retro_nleu_1092, retro_nleu_116, retro_nleu_2225,
Oryctolagus cuniculus	ENSOCUG00000026938	1 retrocopy	retro_ocun_1871,
Otolemur garnettii	ENSOGAG00000006955	4 retrocopies	retro_ogar_1231, retro_ogar_1804, retro_ogar_1857, retro_ogar_289,
Pongo abelii	ENSPPYG00000025949	3 retrocopies	retro_pabe_145, retro_pabe_3616, retro_pabe_534,
Pan troglodytes	ENSPTRG00000006717	3 retrocopies	retro_ptro_3093, retro_ptro_45, retro_ptro_494,