RetrogeneDB ID: retro_cjac_2682

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:150903553..150903945(-)
• Located in intron of: ENSCJAG00000017909

Retrocopy information

• Ensembl ID: ENSCJAG00000017967
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_cjac_2682
AGAGAGGTGCAGTCTGACAAACAAGGCCGACAGGTCGACAGCTGCCCCTACAGCACCGTGGACCTCTCGACACCCGCGGA
CACCAGCTGGAGAAGGACCAATTCTGACTCCGCCCTGCACCAGAGCACAATGATGCCCACACAGCCAGAATCCTTTACCA
GTGGGTCCCAGGACATGCACCAGAAAAGAGTCTTACTGTTAACAGTCCCAGGAATGGAAGAGAACATGTCAGAGGCAGAC
AAAAACCTTTCCAAGCAAGCGTGGCATACCAAGAAGACCGGGTGCAGGCCCAAGTCCTGTGAGGTCCCCGGAATCAACAT
CTTCCCATCCGCCAACCAGGAAAACACTACAGCCCTGATCCCCGCCACCCACAACACTGGGGCTCCCTCCCC

Alignment

ORF - retro_cjac_2682 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.12 %
• Parental protein coverage: 59.55 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RPLSVDKHGRQADSCPYGTVYLSPPADTSWRRTNSDSALHQSTMTPTQPESFTSGSQDVHQKRVLLLTVP
          R....DK.GRQ.DSCPY.TV.LS.PADTSWRRTNSDSALHQSTM.PTQPESFTSGSQD.HQKRVLLLTVP
Retrocopy REVQSDKQGRQVDSCPYSTVDLSTPADTSWRRTNSDSALHQSTMMPTQPESFTSGSQDMHQKRVLLLTVP

Parental  GMEETTSEADKNLSKQAWDTKKTGSRPKSCEVPGINIFPSADQENTTALIPATHNTG-GSLP
          GMEE..SEADKNLSKQAW.TKKTG.RPKSCEVPGINIFPSA.QENTTALIPATHNTG.GSLP
Retrocopy GMEENMSEADKNLSKQAWHTKKTGCRPKSCEVPGINIFPSANQENTTALIPATHNTG<GSLP

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	0.02 RPM	0.95 RPM
SRP051959_heart	0.02 RPM	1.16 RPM
SRP051959_kidney	0.00 RPM	1.13 RPM
SRP051959_liver	0.02 RPM	0.41 RPM
SRP051959_lung	0.00 RPM	1.29 RPM
SRP051959_lymph_node	0.00 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_2682 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2682 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2682 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,