RetrogeneDB ID: retro_cjac_1298

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 14:76139514..76140884(-)
• Located in intron of: ENSCJAG00000003273

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX50
• Ensembl ID: ENSCJAG00000018844
• Aliases: None
• Description: None

Sequence

>retro_cjac_1298
TCAAGGCACTGTTATGACTCAGATGAGAAATCAGAAACAAGAGAAAATGGTGTTACAGGTGACCTGGATGCTCCCAAGGC
CAAAAAAGCTAAAATGACAGAGAAGCTAAATGGAGACACTGAAGAAGGATTTAATAGACTTTCAGATGAATTCTGTAAAT
CTTATAAGTCAAGAAGAAAAGATCTACCAAATGGAGATATTGATGAATATGGAAAAAAGAAATCAAACCAAGTGTCATAC
CTAGATAGTTCTACATATAAATCAAGTGATAATAAATGAGAGAAGGCCTTAATACATAAACAGAAAGAAGGAGCCTTCTC
CAATTTCCCTATTTCTGAAGAGACTATAAAGCTTCTGAAAGGTTGAAGGGTAACATATCTCTTTCCTATTCAAGTTAAGA
CCTTTGGTCCTGTATATGAAGGAAAAGATTTAATAGCTCAAGCACGAACAGGAACAGGAAAGACATTCTCTTTTGCCATC
CCCTTGATTGAAAGACTCCAAAGAAATCAAGACACAATTTTAAAAAGCCACTCACCAAAGGTATTTATTTTGGCTCCAGC
AAGGGAACTGGCAAACCAAGTAGCAAAAGACTTTAAAGATATTACTAGGAAACTCAGAGTGGCATGTTTTTATGATGGAA
CATCATTTCAAAGTCAAATTAACCATATTTGAAATGGTATTGACATCTTTTTTGGAACACTGGTCATATCAAAGACCATC
TGCAGAGTGGCCAATTGGATCTTTCTAAACTGCACTATATTGTGCATGATGAAGTGGATCAAATGTTAAATTTAGGTTTT
GCTGAACAACTTGAAGATATTATTCACAAATCCTACAAAACTAATTCTGAAGACAGTCCTCAGACTTTACTTTTTACTGC
AACTTGCCCACAGTAGGTATACAAAGTTGCAAAAAAATACATGAAATTCAGATATTATCAGGTTTACCTTGTTGGAAAAA
TGACTCAAAAGGCTGCAACTACTGTGGAACCCTTGGCCATCCAGTGTCATTGGTCTCAGAGGCCAGCAGTTATTGGAGAT
GTCTTTCAAGTCTACAGTGGGTCTGAAGGGTGAGCTGTTATTTTCTGGGAGACCAAGAAGAATGTAACTGAAATGGCCGT
GAATCAACACGTAAAACAAAATACCCAGTGTTTACATGGGGACATTGCATAGTCTTAAAGAGAAATTATACAAAAAGGCT
TCAGAGAAGGTAGTTTTAAAGTTTTGGTGGCAACCAATGTGGCTGCCTGTGGTTTGTACATTCCTGAAGTTGACCTGATG
ATTCAAAGTTCTCCTCAGGATGTTGAGTCCTATATCCATCATTCTGGATGCACAAGGAGAGCTGGACGGACAGGGATTTG
TATATGTTTT

Alignment

ORF - retro_cjac_1298 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.75 %
• Parental protein coverage: 62.01 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SRHHYDSDEKSETRENGVTDDLDAPKAKKTKMKEKLNGDTEEGFNRLSDEFSKSHKSRRKDLPNGDIDEY
          SRH.YDSDEKSETRENGVT.DLDAPKAKK.KM.EKLNGDTEEGFNRLSDEF.KS.KSRRKDLPNGDIDEY
Retrocopy SRHCYDSDEKSETRENGVTGDLDAPKAKKAKMTEKLNGDTEEGFNRLSDEFCKSYKSRRKDLPNGDIDEY

Parental  -EKKSKRVSSLDSSTHKSSDNKLEETLTREQKEGAFSNFPISEETIKLLKGRGVTYLFPIQVKTFGPVYE
          ..KKS..VS.LDSST.KSSDNK.E..L...QKEGAFSNFPISEETIKLLKG..VTYLFPIQVKTFGPVYE
Retrocopy GKKKSNQVSYLDSSTYKSSDNK*EKALIHKQKEGAFSNFPISEETIKLLKG*RVTYLFPIQVKTFGPVYE

Parental  GKDLIAQARTGTGKTFSFAIPLIERLQRNQETIKKSRSPKVLVLAPTRELANQVAKDFKDITRKLSVACF
          GKDLIAQARTGTGKTFSFAIPLIERLQRNQ.TI.KS.SPKV..LAP.RELANQVAKDFKDITRKL.VACF
Retrocopy GKDLIAQARTGTGKTFSFAIPLIERLQRNQDTILKSHSPKVFILAPARELANQVAKDFKDITRKLRVACF

Parental  YGGTSYQSQINHIRNGIDILVGT-PGRIKDHLQSGRLDLSKLRHVVLDEVDQMLDLGFAEQVEDIIHESY
          Y.GTS.QSQINHI.NGIDI..GT..G.IKDHLQSG.LDLSKL...V.DEVDQML.LGFAEQ.EDIIH.SY
Retrocopy YDGTSFQSQINHI*NGIDIFFGT<TGHIKDHLQSGQLDLSKLHYIVHDEVDQMLNLGFAEQLEDIIHKSY

Parental  KTDSEDNPQTLLFSATCPQWVYKVAKKYMKSRYEQVDLVGKMTQKAATTVEHLAIQCHWSQRPAVIGDVL
          KT.SED.PQTLLF.ATCPQ.VYKVAKKYMK.RY.QV.LVGKMTQKAATTVE.LAIQCHWSQRPAVIGDV.
Retrocopy KTNSEDSPQTLLFTATCPQ*VYKVAKKYMKFRYYQVYLVGKMTQKAATTVEPLAIQCHWSQRPAVIGDVF

Parental  QVYSGSEGRAIIFCETKKNVTEMAMNPHIKQNAQCLHGDIAQSQREITLKGFREGSFKVLVATNVAARGL
          QVYSGSEG.A.IF.ETKKNVTEMA.N.H.KQN.QCLHGDIA.S.REI..KGFREGSFKVLVATNVAA.GL
Retrocopy QVYSGSEG*AVIFWETKKNVTEMAVNQHVKQNTQCLHGDIA*S*REIIQKGFREGSFKVLVATNVAACGL

Parental  DIPEVDLVIQSSPPQDVESYIHRSGRTGRAGRTGICICF
          .IPEVDL.IQSS.PQDVESYIH.SG.T.RAGRTGICICF
Retrocopy YIPEVDLMIQSS-PQDVESYIHHSGCTRRAGRTGICICF

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	0.95 RPM	19.10 RPM
SRP051959_heart	0.84 RPM	20.98 RPM
SRP051959_kidney	1.26 RPM	20.61 RPM
SRP051959_liver	0.78 RPM	18.78 RPM
SRP051959_lung	0.94 RPM	19.85 RPM
SRP051959_lymph_node	1.05 RPM	27.78 RPM
SRP051959_skeletal_muscle	1.07 RPM	18.54 RPM
SRP051959_spleen	0.69 RPM	24.71 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1298 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1298 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1298 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009966	2 retrocopies	retro_cjac_3639, retro_cjac_3640,
Callithrix jacchus	ENSCJAG00000012876	1 retrocopy	retro_cjac_1912,
Callithrix jacchus	ENSCJAG00000018844	1 retrocopy	retro_cjac_1298 ,
Homo sapiens	ENSG00000107625	2 retrocopies	retro_hsap_2089, retro_hsap_2866,
Macaca mulatta	ENSMMUG00000001006	1 retrocopy	retro_mmul_982,
Mus musculus	ENSMUSG00000020076	1 retrocopy	retro_mmus_3362,
Nomascus leucogenys	ENSNLEG00000011631	2 retrocopies	retro_nleu_1300, retro_nleu_609,
Otolemur garnettii	ENSOGAG00000001844	2 retrocopies	retro_ogar_1492, retro_ogar_555,
Pongo abelii	ENSPPYG00000002390	3 retrocopies	retro_pabe_2007, retro_pabe_2369, retro_pabe_2418,
Pan troglodytes	ENSPTRG00000002562	2 retrocopies	retro_ptro_1536, retro_ptro_1938,