RetrogeneDB ID: retro_cjac_2474

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:127604876..127605215(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CNIH4
• Ensembl ID: ENSCJAG00000008013
• Aliases: None
• Description: cornichon homolog 4 (Drosophila) [Source:HGNC Symbol;Acc:25013]

Sequence

>retro_cjac_2474
GAGGACATAGTCTTTGTTTTCTCTCTCCTCAGTTGTTGCAGGATCACTTTTCTCTCAGTCTTCATAATTACATTGTCTAA
TTTAGAGTGTGATTACATTAATGCTAGATCTAGATCATGTTGCTCAAAATTAAATAAGTAGGTACTTCCAAGATTGATTG
GTCATATTATTGTCACTGTATTAATGCGCATTTTGTTGCACTGGTTCATCTTCCTCCTCAGCTTACCTATTGCCACTTGG
AATATATATTGATTCATTATGGTGCCAAGCAGTAACATAAGAGTATTTGATCCAACAGGAATACACAATCAAGGACAGCT
AAAGTCACATAGGAAAGAC

Alignment

ORF - retro_cjac_2474 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.44 %
• Parental protein coverage: 80.58 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EAVVFVFSLLDCCALIFLSVYFIITLSDLECDYINA--RSCCSKLNKWVIPELIGHTVVTVLMLISLHWF
          E..VFVFSLL.CC...FLSV.FIITLS.LECDYINA..RSCCSKLNK.V.P.LIGH..VTVLM.I.LHWF
Retrocopy EDIVFVFSLLSCCRITFLSV-FIITLSNLECDYINARSRSCCSKLNK*VLPRLIGHIIVTVLMRILLHWF

Parental  IFLLNLPVATWNIYRYIMVPSGNMGVFDPTEIHNRGQLKSHMKE
          IFLL.LP.ATWNIY..IMVPS.N..VFDPT.IHN.GQLKSH.K.
Retrocopy IFLLSLPIATWNIY*FIMVPSSNIRVFDPTGIHNQGQLKSHRKD

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	3.35 RPM
SRP051959_heart	0.02 RPM	3.60 RPM
SRP051959_kidney	0.00 RPM	11.96 RPM
SRP051959_liver	0.00 RPM	3.27 RPM
SRP051959_lung	0.00 RPM	5.06 RPM
SRP051959_lymph_node	0.00 RPM	4.66 RPM
SRP051959_skeletal_muscle	0.00 RPM	3.25 RPM
SRP051959_spleen	0.00 RPM	4.56 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2474 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2474 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2474 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006544	1 retrocopy	retro_chof_327,
Callithrix jacchus	ENSCJAG00000007306	1 retrocopy	retro_cjac_103,
Callithrix jacchus	ENSCJAG00000008013	1 retrocopy	retro_cjac_2474 ,
Cavia porcellus	ENSCPOG00000007310	1 retrocopy	retro_cpor_777,
Dasypus novemcinctus	ENSDNOG00000007093	1 retrocopy	retro_dnov_1669,
Homo sapiens	ENSG00000143771	1 retrocopy	retro_hsap_3656,
Gorilla gorilla	ENSGGOG00000005708	1 retrocopy	retro_ggor_2470,
Myotis lucifugus	ENSMLUG00000003134	1 retrocopy	retro_mluc_1314,
Macaca mulatta	ENSMMUG00000009936	1 retrocopy	retro_mmul_1796,
Nomascus leucogenys	ENSNLEG00000013549	1 retrocopy	retro_nleu_514,
Ochotona princeps	ENSOPRG00000001589	1 retrocopy	retro_opri_749,
Pongo abelii	ENSPPYG00000000183	1 retrocopy	retro_pabe_3003,
Pan troglodytes	ENSPTRG00000002025	1 retrocopy	retro_ptro_2481,
Pteropus vampyrus	ENSPVAG00000014034	1 retrocopy	retro_pvam_692,
Ictidomys tridecemlineatus	ENSSTOG00000027396	2 retrocopies	retro_itri_1502, retro_itri_1552,
Vicugna pacos	ENSVPAG00000012521	2 retrocopies	retro_vpac_180, retro_vpac_215,