RetrogeneDB ID: retro_cjac_666

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 10:24900612..24901522(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CRTC1
• Ensembl ID: ENSCJAG00000007421
• Aliases: None
• Description: None

Sequence

>retro_cjac_666
CGGCACCGCCGGCCCCTATCAGTGGACAAACACGGACCGCAGGCCGACAGCTGCCCCTACGACACCATGTACCTCTTGCC
ACCCGCGGACACCAGCTGGAGAAGGACCAATTCTGCCTCCGCCCTGCACCAGAGCACAATGAGGCCCACACAGCCAGAAT
CCTTTACCAGTGGGTCCCCAGACCTGCACAAGAAAAGAGTCTTATTGTTAACAGTCCCAGGAATGGAAGAGACCACATCA
GTGGCAGACAAAAACCTTCCCAAGCAAGCGTGGGACTCCAAGAAGACGGGGGCCAGGCCCAAGTCCTGTGAGGTCCCCTG
AATCAACATCATCTTTTCGGCCGACCAGGAAAACACCACAGCCCTGATCCCCGCCACTCACAACACTGGGGGATCCGTGC
CTGACCTGACCAACATTCACTTCCTCTCCCCGCTCCCGACCCTGCTGGACCCCGAGGAGCCCACCTTCCCCGCGCTGAGC
AGCTCCACCAGCACCGGCAACCTCGTGGCCAACCTGACGCACCTGGGCATTGGCGGCGCCAGCCCGTGATGAGCACACCT
GGGTCCTTTCCGCAACACCACCCAGCCGGCATCAGCCCCCTGTCCCTGAGCACAGAGGCGAGGCGTCAGCAGGCATCGCC
CACCCTGTCCCCACTGGCACCCATCACTCAGGCCGTGGCCATGGATGCCCTGTCTCTAGAGCAGCAGCTGCCCTACGCCT
TCTTCACCTAGGCGGGCTCCCAGCAGCCGCCGTCCCCACCATCCCCGCAGGTGTCCGTCCACTTGTCCCCCCCACCCCCG
CGGCCCCCTGTTGCCCAGCGCCAGCCTGACTCTTGGGCCACAGCCACCCCCGCTCGCGGTCACGGTACCGTCCTCTCTCC
CCCAGTCTCCCCCAGAGAACCCCAGACAGC

Alignment

ORF - retro_cjac_666 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.19 %
• Parental protein coverage: 72.1 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KHGRQISFSPED-EAD-CPYGTVYLSPPADTSWRRTNSDSALHQSTMTPTQPESFTSGSQDVHQKRVLLL
          .H.R..S.......AD.CPY.T.YL.PPADTSWRRTNS.SALHQSTM.PTQPESFTSGS.D.H.KRVLLL
Retrocopy RHRRPLSVDKHGPQADSCPYDTMYLLPPADTSWRRTNSASALHQSTMRPTQPESFTSGSPDLHKKRVLLL

Parental  TVPGMEETTSEADKNLSKQAWDTKKTGSRPKSCEVPGINIFPSADQENTTALIPATHNTGGSLPDLTNIH
          TVPGMEETTS.ADKNL.KQAWD.KKTG.RPKSCEVP.INI..SADQENTTALIPATHNTGGS.PDLTNIH
Retrocopy TVPGMEETTSVADKNLPKQAWDSKKTGARPKSCEVP*INIIFSADQENTTALIPATHNTGGSVPDLTNIH

Parental  FPSPLPTPLDPEEPTFPSLSGSSSTGNLAANLTHLGIGGAG-QGMSTPGSSPQHRPAGVSPLSLSTEARR
          F.SPLPT.LDPEEPTFP.LS.S.STGNL.ANLTHLGIGGA....MSTPGS.PQH.PAG.SPLSLSTEARR
Retrocopy FLSPLPTLLDPEEPTFPALSSSTSTGNLVANLTHLGIGGAS<PVMSTPGSFPQHHPAGISPLSLSTEARR

Parental  QQASPTLSPLSPITQAVAMDALSLEQQLPYAFFTQAGSQQPPPQPQPPPPPPPASQQPPPPPPPQASVRL
          QQASPTLSPL.PITQAVAMDALSLEQQLPYAFFT.AGSQQPP....PP.P.......PPPP.PP.A..R.
Retrocopy QQASPTLSPLAPITQAVAMDALSLEQQLPYAFFT*AGSQQPP---SPPSPQVSVHLSPPPPRPPVAQ-RQ

Parental  PPG-GPLLPSASLT-RGPQPPPLAVTVPSS
          P...GP..P....T...P..P.L....P.S
Retrocopy PDS>GPQPPPLAVT>YRPLSPSLPQRTPDS

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	0.95 RPM
SRP051959_heart	0.00 RPM	1.16 RPM
SRP051959_kidney	0.00 RPM	1.13 RPM
SRP051959_liver	0.00 RPM	0.41 RPM
SRP051959_lung	0.00 RPM	1.29 RPM
SRP051959_lymph_node	0.02 RPM	1.44 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.87 RPM
SRP051959_spleen	0.00 RPM	1.20 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_666 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_666 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_666 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007421	3 retrocopies	retro_cjac_2682, retro_cjac_595, retro_cjac_666 ,
Homo sapiens	ENSG00000105662	1 retrocopy	retro_hsap_2102,
Pan troglodytes	ENSPTRG00000010719	1 retrocopy	retro_ptro_1542,