RetrogeneDB ID: retro_cjac_4145

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:26638314..26639059(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDCA5
• Ensembl ID: ENSCJAG00000002502
• Aliases: None
• Description: cell division cycle associated 5 [Source:HGNC Symbol;Acc:14626]

Sequence

>retro_cjac_4145
ATGTCTTGGAGGCGAACGCGGCCCAGAGGGGCCGCGCAGCGCTCCGGGCCAAGGGCCCCATCTCCTACTAAGTCTGTGCG
GAGGTCCCAACAGAAATCAGGCTCTGATCTCCCAAGCATGCCCCCTGAAATCTGGCCGAAGACACCCAGTGCGGCTGCAA
TCAGAAAGCCCATCGTCTTGGAGATCGTGGCCCAAGATGTAGACGTCCCAGCTGTTCCCTTGCCTCGCAGGAGCCCTAGG
ATTGCCTTTTTCTTGGAGAAGGAAAACAAGCCCCCTTGCAAGGAGCTGACTAAGGAGGACCTTTCCAAGATACAGCCTCC
CTGCCACTCCTAACACTTCTCCTGTGCTCAACCCTGAGGCTGAGTCCAGCTCCAAGGAGAGAGAGCTGGAGGCCAAATAC
TTGGAAATGTTTAAGAAAGTCAGGGGCTCCTACAGCCGGCTGGAGACCCTGGGCTCTGCCTCCACCTCCACCCCAGGCTG
CCGGTTCTGCTTTGGCTTCCATGGGCTACTAGGGGCAGAAGATTTGTCCGGAGTCTCACCAGTGGTGTGCTCAAAATTCA
CCGAGGTCCCCAGGGTCGGTACAAAGCCCTGAGCCACAGACACAATTCTCCCTGGAATCTCTCCACCACCCGAGAAACAG
AAACAAAAGAAGATGCTAGAGATACTGAAAACGGAGCTGGATGAGAGGGCTGCAGCCATGAATGCTGAGTTTGAAGCTGC
TGAGCAGTTTGATCTCCTGGTTGAA

Alignment

ORF - retro_cjac_4145 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.45 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPGRRTRSGGAAQRSGPRAPSPVKSVRRSQRKSGSDLPSIPPEIWPKTPSAAAIRKPIVLKKIVAHAVEV
          M..RRTR..GAAQRSGPRAPSP.KSVRRSQ.KSGSDLPS.PPEIWPKTPSAAAIRKPIVL..IVA..V.V
Retrocopy MSWRRTRPRGAAQRSGPRAPSPTKSVRRSQQKSGSDLPSMPPEIWPKTPSAAAIRKPIVLE-IVAQDVDV

Parental  PAVHSPRRSPRIAFFLE-KENKPPCRELTKEDLSKIHSVPDTPNTSPVLNPEAESSSKERELDARDLEMF
          PAV..PRRSPRIAFFLE.....P..R...........S.P.TPNTSPVLNPEAESSSKEREL.A..LEMF
Retrocopy PAVPLPRRSPRIAFFLE>RKTSPLARS*LRRTFPR-YSLPATPNTSPVLNPEAESSSKERELEAKYLEMF

Parental  KKVRRSYSRLETLGSTSTSTPGRRSCFGFEGLLGAEDLSGVSPVVCSKFIEVPRVGAKPWAPDTTLPGIS
          KKVR.SYSRLETLGS.STSTPG.R.CFGF.GLLGAEDLSGVSPVVCSKF.EVPRVG.KP.A.DT.LPGIS
Retrocopy KKVRGSYSRLETLGSASTSTPGCRFCFGFHGLLGAEDLSGVSPVVCSKFTEVPRVGTKP*ATDTILPGIS

Parental  PPPEKQKRKKKKMPEILKTELDEWAAAMNAEFEAAEQFDLLVE
          PPPEKQ..K.KKM.EILKTELDE.AAAMNAEFEAAEQFDLLVE
Retrocopy PPPEKQ--KQKKMLEILKTELDERAAAMNAEFEAAEQFDLLVE

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	1.55 RPM
SRP051959_heart	0.00 RPM	0.00 RPM
SRP051959_kidney	0.00 RPM	0.02 RPM
SRP051959_liver	0.00 RPM	0.11 RPM
SRP051959_lung	0.00 RPM	0.34 RPM
SRP051959_lymph_node	0.00 RPM	0.78 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.07 RPM
SRP051959_spleen	0.00 RPM	0.38 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4145 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4145 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4145 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
Callithrix jacchus	ENSCJAG00000002502	1 retrocopy	retro_cjac_4145 ,
Dasypus novemcinctus	ENSDNOG00000019033	1 retrocopy	retro_dnov_2601,
Felis catus	ENSFCAG00000028197	1 retrocopy	retro_fcat_761,
Pteropus vampyrus	ENSPVAG00000007908	1 retrocopy	retro_pvam_567,
Rattus norvegicus	ENSRNOG00000046635	2 retrocopies	retro_rnor_639, retro_rnor_640,