RetrogeneDB ID: retro_cjac_2674

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:139101416..139101863(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EMD
• Ensembl ID: ENSCJAG00000011853
• Aliases: None
• Description: None

Sequence

>retro_cjac_2674
GTGGATTCAGATATGTATGATCTTCCCAAGAAAGAGGACGCCTTACTCTACCAGAGCAAGGGCTACAGTGACGACTACTA
TGAAGAGAGCTACTTAACTACCAGGATTTATGGGGAGCCCGACTCTGCGGGCCAGTCCAGGGGCTTCCACCAGTCTGCGA
CTTCACTCCCAGATGCTGACACTTTCCATCACCAGGTGCGTGATGACAATCTTTTGTCGTCTTCTGAAGAGGAGTGCGAG
GATAGGGAATGCCCCATGTGCGGCTGGGACAGTGGCTACCAGAGCATCGCAGACTACCGCCCTGTTTCATCCTCCAGGAG
CTCCCTGGGCCTGTCCTATTATCCTACCTCCTCCACCTCTTCTGTGTCCTAATCATCTTCCCCTTCATGGCTTACCCGCC
GAGGCATCCGGCCAGAAAAGCATGCTCCTGGGGCCGGGCTTGGCCAC

Alignment

ORF - retro_cjac_2674 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.07 %
• Parental protein coverage: 58.82 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VDSDMYDLPKKEDALLYQSKGYNDDYYEESYLTTRTYGEPDSAGQSRGFRQSATSLPDADTFHHQVRDDN
          VDSDMYDLPKKEDALLYQSKGY.DDYYEESYLTTR.YGEPDSAGQSRGF.QSATSLPDADTFHHQVRDDN
Retrocopy VDSDMYDLPKKEDALLYQSKGYSDDYYEESYLTTRIYGEPDSAGQSRGFHQSATSLPDADTFHHQVRDDN

Parental  LLSS-EEECKDRERPMYGRDSAYQSIAHYRPVSASRSSLGLSYYPTSSSTSSVSSSSSSPSWLTRRAIRP
          LLSS.EEEC.DRE.PM.G.DS.YQSIA.YRPVS.SRSSLGLSYYPT.SSTSSV.S.SSSPSWLTRR.IRP
Retrocopy LLSSSEEECEDRECPMCGWDSGYQSIADYRPVSSSRSSLGLSYYPT-SSTSSV-S*SSSPSWLTRRGIRP

Parental  EKHAPGAGLGH
          EKHAPGAGLGH
Retrocopy EKHAPGAGLGH

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	5.52 RPM
SRP051959_heart	0.07 RPM	5.37 RPM
SRP051959_kidney	0.07 RPM	4.19 RPM
SRP051959_liver	0.02 RPM	3.44 RPM
SRP051959_lung	0.03 RPM	5.35 RPM
SRP051959_lymph_node	0.00 RPM	5.82 RPM
SRP051959_skeletal_muscle	0.00 RPM	5.28 RPM
SRP051959_spleen	0.00 RPM	4.87 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2674 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2674 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2674 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000011853	1 retrocopy	retro_cjac_2674 ,
Tursiops truncatus	ENSTTRG00000013924	1 retrocopy	retro_ttru_314,