RetrogeneDB ID: retro_cjac_3033

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:142540783..142541074(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: OOEP
• Ensembl ID: ENSCJAG00000009962
• Aliases: None
• Description: None

Sequence

>retro_cjac_3033
TGGTGGTTTCCGGTGCAGGAACTGAGAGACCCTTCGGTGTCCTACCTGGAGGTATGTCTGGCAGTTGTGATATCTGGCAC
AGACAGAGCCGTAATTCCAGAACTGGAGTAGATGAGCCATGCGCTGCTGATGGTGGACATAGTGGACTCCAGAATCCAAG
TGGAAATCACAGTTTTTGGACACCTCTGTGTAGAGAATCAGGTTAAGACCGTGTTCCCACACTTGTCATGGCTTCACCAA
CAATATGCTTGAGCCGAGAAAATAAAACACCTTGAGGAGAACTTGAAGGCT

Alignment

ORF - retro_cjac_3033 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.24 %
• Parental protein coverage: 65.77 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  WWFPVQELRNPLVFYLETWLADVLFGPDRAIIPEMEWTSQALLTVDIVDSGNLVEITVFGRPRVQNRVKS
          WWFPVQELR.P.V.YLE..LA.V..G.DRA.IPE.E..S.ALL.VDIVDS...VEITVFG...V.N.VK.
Retrocopy WWFPVQELRDPSVSYLEVCLAVVISGTDRAVIPELE*MSHALLMVDIVDSRIQVEITVFGHLCVENQVKT

Parental  MLLCLAWFHREHRARAEKMKHLEKNLKA
          ....L.W.H....A.AEK.KHLE.NLKA
Retrocopy VFPHLSWLHQQY-A*AEKIKHLEENLKA

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	0.00 RPM
SRP051959_heart	0.00 RPM	0.00 RPM
SRP051959_kidney	0.00 RPM	0.00 RPM
SRP051959_liver	0.00 RPM	0.00 RPM
SRP051959_lung	0.00 RPM	0.00 RPM
SRP051959_lymph_node	0.00 RPM	0.00 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.00 RPM
SRP051959_spleen	0.00 RPM	0.00 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3033 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3033 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3033 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_432
Pan troglodytes	retro_ptro_329
Gorilla gorilla	retro_ggor_422
Macaca mulatta	retro_mmul_519

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009947	1 retrocopy	retro_cjac_1153,
Callithrix jacchus	ENSCJAG00000009962	1 retrocopy	retro_cjac_3033 ,
Homo sapiens	ENSG00000203907	3 retrocopies	retro_hsap_432, retro_hsap_4807, retro_hsap_543,
Gorilla gorilla	ENSGGOG00000016832	3 retrocopies	retro_ggor_2992, retro_ggor_422, retro_ggor_495,
Loxodonta africana	ENSLAFG00000012754	2 retrocopies	retro_lafr_412, retro_lafr_782,
Myotis lucifugus	ENSMLUG00000017174	2 retrocopies	retro_mluc_115, retro_mluc_252,
Macaca mulatta	ENSMMUG00000000416	2 retrocopies	retro_mmul_2561, retro_mmul_519,
Nomascus leucogenys	ENSNLEG00000001204	2 retrocopies	retro_nleu_2182, retro_nleu_717,
Oryctolagus cuniculus	ENSOCUG00000025904	1 retrocopy	retro_ocun_20,
Pan troglodytes	ENSPTRG00000029545	3 retrocopies	retro_ptro_3197, retro_ptro_329, retro_ptro_408,
Rattus norvegicus	ENSRNOG00000025957	1 retrocopy	retro_rnor_2192,
Tursiops truncatus	ENSTTRG00000001487	2 retrocopies	retro_ttru_1376, retro_ttru_1803,