RetrogeneDB ID: retro_cjac_1753

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 19:40056264..40056509(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000037004
• Aliases: None
• Description: None

Sequence

>retro_cjac_1753
CGCCAGGCAGGAGAGGAAGAGGCAGTGACCCTGAGCGGCCTGGGAATGTGGTGAGTGTGGTGTTTGTAGATCCGTCAGGC
TGGCGGATTCCAGTGAGCAGTAGAGTCAGGGACAGTGTTGTCCACCTGACCCCATGCCATGGGGTAAACGTGGAAAGCAC
CTGTGAAGCCTTCCTAGCATGCTCCACCTGCCATGTGCATGTGAGCAAAGACCGCCTGGACCTTCTGTCTCCTCCTGAAA
AGAGG

Alignment

ORF - retro_cjac_1753 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.88 %
• Parental protein coverage: 56.64 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RQAGE-EA-GGPERPGDVVNVVFVDRSGQRIPVSGRVGDNVLHLAQRHGVDLEGACEASLACSTCHVYVS
          RQAGE.EA...PERPG.VV.VVFVD.SG.RIPVS.RV.D.V.HL...HGV..E..CEA.LACSTCHV.VS
Retrocopy RQAGEEEA<SDPERPGNVVSVVFVDPSGWRIPVSSRVRDSVVHLTPCHGVNVESTCEAFLACSTCHVHVS

Parental  EDHLDLLPPPEER
          .D.LDLL.PPE.R
Retrocopy KDRLDLLSPPEKR

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	1.26 RPM
SRP051959_heart	0.00 RPM	2.21 RPM
SRP051959_kidney	0.00 RPM	2.86 RPM
SRP051959_liver	0.00 RPM	3.12 RPM
SRP051959_lung	0.00 RPM	2.91 RPM
SRP051959_lymph_node	0.00 RPM	2.40 RPM
SRP051959_skeletal_muscle	0.00 RPM	1.79 RPM
SRP051959_spleen	0.00 RPM	2.00 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1753 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1753 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1753 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_331
Pan troglodytes	retro_ptro_267
Gorilla gorilla	retro_ggor_355
Macaca mulatta	retro_mmul_584

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010395	1 retrocopy	retro_cjac_2028,
Callithrix jacchus	ENSCJAG00000037004	1 retrocopy	retro_cjac_1753 ,
Homo sapiens	ENSG00000267673	1 retrocopy	retro_hsap_331,