RetrogeneDB ID: retro_cjac_3555

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: ACFV01184347.1:5954..6233(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000001008
• Aliases: None
• Description: None

Sequence

>retro_cjac_3555
TTCATAAGAGTTCTTATCATAGCACTTAAACTGAGCTAAATCAAAGGCCAGTGTTCTGTTTTGCAGGTGTACATCCAAAG
ACTTATACAGTGTGCTCCTATGTACATTCGTCCAACCACCTGGAGGAGGATTATCCTCGGAGCCTTTCTTCTTGTCATCA
AGGTTGGGAGCAATGTGGCTGTGTGCAATGAGGATTTATGCATGCGCTTTGAGAAAACTACAGTTGACGATCTGTGAGTT
TGTATGGTTTTTGTGAACTTTCTAACCATTTTTGGATAC

Alignment

ORF - retro_cjac_3555 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.06 %
• Parental protein coverage: 54.27 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FIRTLFYVKKLK--VADAIITMVYIQRLIQYAHIYICSATWRRIILGAILVVIKVRSNVAVCNRDLCRRF
          FIR.L....KL...........VYIQRLIQ.A..YI...TWRRIILGA.L.VIKV.SNVAVCN.DLC.RF
Retrocopy FIRVLIIALKLS*IKGQCSVLQVYIQRLIQCAPMYIRPTTWRRIILGAFLLVIKVGSNVAVCNEDLCMRF

Parental  EKTTVNDLNKLEMY--FLRLIGY
          EKTTV.DL........FL...GY
Retrocopy EKTTVDDL*VCMVFVNFLTIFGY

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	3.13 RPM	1.29 RPM
SRP051959_heart	1.77 RPM	1.28 RPM
SRP051959_kidney	3.17 RPM	2.44 RPM
SRP051959_liver	1.10 RPM	1.62 RPM
SRP051959_lung	3.53 RPM	1.74 RPM
SRP051959_lymph_node	3.90 RPM	2.31 RPM
SRP051959_skeletal_muscle	0.94 RPM	1.03 RPM
SRP051959_spleen	3.09 RPM	1.66 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3555 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3555 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3555 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001008	1 retrocopy	retro_cjac_3555 ,
Callithrix jacchus	ENSCJAG00000002901	1 retrocopy	retro_cjac_569,
Callithrix jacchus	ENSCJAG00000011445	1 retrocopy	retro_cjac_1164,
Callithrix jacchus	ENSCJAG00000034702	1 retrocopy	retro_cjac_610,
Homo sapiens	ENSG00000163249	3 retrocopies	retro_hsap_1629, retro_hsap_1984, retro_hsap_4845,
Mus musculus	ENSMUSG00000070871	1 retrocopy	retro_mmus_3072,