RetrogeneDB ID: retro_cjac_1223

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 14:73177217..73177428(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000013936
• Aliases: None
• Description: None

Sequence

>retro_cjac_1223
ATGATCAGAGACATCCTACTGTTTGGGATGTTGCTGATGAATGCTGGGGCAGGGCTCAACTTTAAACTGAAAAAAAGGAC
ATGCAAGGTTTTGGGAAGGAGGTGTGGAAGCACAGCACAGGTGACAACATTAGGGAATTCTTACTGAGCCTCAGATATTT
TGAGTCTTCATCATCCTGTGGAACGTCTTTATGATGTGCTACATGATTATG

Alignment

ORF - retro_cjac_1223 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.34 %
• Parental protein coverage: 68.93 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MIGDILLFGTLLMNAGAVLNFKLKK-KDTQGFGEESREPSTGDNIREFLLSLRYFR-IFIALWNIFMMFC
          MI.DILLFG.LLMNAGA.LNFKLKK.KD.QGFG.E....STGDNIREFLLSLRYF...FI.LWN.FMM..
Retrocopy MIRDILLFGMLLMNAGAGLNFKLKK<KDMQGFGKEVWKHSTGDNIREFLLSLRYFE<VFIILWNVFMMCY

Parental  MIV
          MI.
Retrocopy MIM

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	5.64 RPM
SRP051959_heart	0.00 RPM	6.86 RPM
SRP051959_kidney	0.00 RPM	7.61 RPM
SRP051959_liver	0.00 RPM	10.46 RPM
SRP051959_lung	0.00 RPM	7.71 RPM
SRP051959_lymph_node	0.00 RPM	6.32 RPM
SRP051959_skeletal_muscle	0.00 RPM	5.02 RPM
SRP051959_spleen	0.00 RPM	7.37 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1223 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1223 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1223 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010105	1 retrocopy	retro_amel_1688,
Canis familiaris	ENSCAFG00000015643	1 retrocopy	retro_cfam_1927,
Callithrix jacchus	ENSCJAG00000013936	1 retrocopy	retro_cjac_1223 ,
Equus caballus	ENSECAG00000026861	1 retrocopy	retro_ecab_640,
Felis catus	ENSFCAG00000016411	1 retrocopy	retro_fcat_934,
Homo sapiens	ENSG00000214046	1 retrocopy	retro_hsap_2244,
Mus musculus	ENSMUSG00000044600	1 retrocopy	retro_mmus_450,
Nomascus leucogenys	ENSNLEG00000005569	1 retrocopy	retro_nleu_1315,
Pongo abelii	ENSPPYG00000009694	2 retrocopies	retro_pabe_1964, retro_pabe_2031,
Pan troglodytes	ENSPTRG00000010650	1 retrocopy	retro_ptro_1589,
Rattus norvegicus	ENSRNOG00000042037	1 retrocopy	retro_rnor_2694,
Sus scrofa	ENSSSCG00000013863	1 retrocopy	retro_sscr_955,
Tarsius syrichta	ENSTSYG00000009556	1 retrocopy	retro_tsyr_1550,
Tursiops truncatus	ENSTTRG00000015020	2 retrocopies	retro_ttru_136, retro_ttru_597,
Vicugna pacos	ENSVPAG00000006699	1 retrocopy	retro_vpac_65,