RetrogeneDB ID: retro_cjac_2271

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:124722910..124724000(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX59
• Ensembl ID: ENSCJAG00000005183
• Aliases: None
• Description: None

Sequence

>retro_cjac_2271
TATGAGGTGTCAATCCCCATCCAAATACAGATGATTCCTGTGGGACTTCTGGGAAGAGACATTCTGGCCAGTGCAGATAC
TGGCTCAGGAAAAACAGCTGTTTTTCTTCTTTCTGTTATCATGCAAGCTTTATTTGAGAGCAAAACTCCATTTGCACTCA
TTCTTACACCAACCAGAGAGTTAGCCATTCAGCTGGTTAGACAAACTAAAGAATTGATGAGTGGCCTTCCACACATGAAA
ACCGTGCTTCTTGTATGGGACTTACCCTTACCCCCACAGCTTTATCGTCTGCAACATGTTAAGGTTATTATAGCAACCCC
TGAGCGACTTCTGGATATAATAAACTAGAGCTCTGTAGAACTCTGTGGTATAAAGATTGGTAGTAGATGAAGCTGATACC
ATGTTAGAGATGGGCTTTCAACAAGTGCTTGACATTTTGGAAAATGTTCCTATTGATTGTCAGACCATTTTGGTTTCGGC
CACAATTCCAACTAGCATAGAACAACTAGTAAGCCATTGTCTGCATAATCCTGTGAGAATTATAACTGGAGAAAAGAATC
TACCTTGTGTCAATGTGCACAAGATTATTGTGGGTAGAAGACCCAGCCAAAAAGAAAAAATTATTTGAAATTTTAAATGA
TAAGAAATTATTTAGCTTCCAGTGTTAGTATTTGTGGACAGCAAAGTAGGAGTAGATCTGTTGAGTGAAGCCATTCAGAA
AATCACAGGGCGGAAAAGTGTATCTATACATTCAGAGAAGTCACAAATATAAAGGAAAAATATATTGAAGGGACTACTTG
AAGGAGACTGTGAAGGTGCAGTGAGCACAGGAGTCTTGGGATGAGGACTAGACTTGATCAGTGTCTGGCTGGTTGTCAAT
TTTGGTATGCCTTCAGGAATGGACAAGTACGTCCATCAGGTTGGAAGAGTAGGCAGATTAGGTCAAAAGGAAACAGCAAT
TACTTTCATCAATAATAATTCAAAAAGACTCTTCTGGGATATTGCAAAACGAGTAAATCCCACAGGATCCATTCTTCCCC
CACGGTTATTAAATTCCCCATACCTTCATGACTAGAGGAAAAAGGATCAA

Alignment

ORF - retro_cjac_2271 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.16 %
• Parental protein coverage: 59.19 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  YEVPTPIQMQMIPVGLLGRDILASADTGSGKTAAFLLPVIMRALFERKTPSALILTPTRELAIQIERQAK
          YEV..PIQ.QMIPVGLLGRDILASADTGSGKTA.FLL.VIM.ALFE.KTP.ALILTPTRELAIQ..RQ.K
Retrocopy YEVSIPIQIQMIPVGLLGRDILASADTGSGKTAVFLLSVIMQALFESKTPFALILTPTRELAIQLVRQTK

Parental  ELMSGLPRMKTVLLVGGLPLPPQLYRLQQHVKVIIATPGRLLDIMKQSSVELCGIKI-VVVDEADTMLKM
          ELMSGLP.MKTVLLV..LPLPPQLYRL.QHVKVIIATP.RLLDI...SSVELCGIKI.VV.DEADTML.M
Retrocopy ELMSGLPHMKTVLLVWDLPLPPQLYRL-QHVKVIIATPERLLDIIN*SSVELCGIKI>VV-DEADTMLEM

Parental  GFQQQVLDILENIPNDCQTILVSATIPTSIEQLASQLLHNPVRIITGEENLPCANVRQIILWVEDPAKK-
          GF.QQVLDILEN.P.DCQTILVSATIPTSIEQL.S..LHNPVRIITGE.NLPC.NV..II.....P..K.
Retrocopy GF-QQVLDILENVPIDCQTILVSATIPTSIEQLVSHCLHNPVRIITGEKNLPCVNVHKIIVG-RRPSQK>

Parental  KKLFEILNDKKLFK-PPVLVFVDCKLGADLLSEAVQKITGLKSISIHSEKSQIERKNILKGLLEGDFEVV
          KKLFEILNDKKLF...PVLVFVD.K.G.DLLSEA.QKITG.KS.SIHSEKSQI.RKNILKGLLEGD.E..
Retrocopy KKLFEILNDKKLFS<LPVLVFVDSKVGVDLLSEAIQKITGRKSVSIHSEKSQI*RKNILKGLLEGDCEGA

Parental  VSTGVLGRGLDLISVRLVVNFDMPSSMDEYVHQVGRVGRLGQNGTAITFINNNSKRLFWDIAKRVKPTGS
          VSTGVLG.GLDLISV.LVVNF.MPS.MD.YVHQVGRVGRLGQ..TAITFINNNSKRLFWDIAKRV.PTGS
Retrocopy VSTGVLG*GLDLISVWLVVNFGMPSGMDKYVHQVGRVGRLGQKETAITFINNNSKRLFWDIAKRVNPTGS

Parental  ILPPQLLNSPYLHDQKRKEQ
          ILPP.LLNSPYLHD...K.Q
Retrocopy ILPPRLLNSPYLHD*RKKDQ

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	6.23 RPM
SRP051959_heart	0.00 RPM	5.53 RPM
SRP051959_kidney	0.00 RPM	6.54 RPM
SRP051959_liver	0.00 RPM	4.68 RPM
SRP051959_lung	0.00 RPM	7.42 RPM
SRP051959_lymph_node	0.00 RPM	5.52 RPM
SRP051959_skeletal_muscle	0.00 RPM	4.54 RPM
SRP051959_spleen	0.00 RPM	5.99 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2271 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2271 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2271 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005183	1 retrocopy	retro_cjac_2271 ,