RetrogeneDB ID: retro_cjac_338

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:5838620..5839130(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000034032
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: HDGF
• Ensembl ID: ENSCJAG00000006157
• Aliases: None
• Description: hepatoma-derived growth factor [Source:HGNC Symbol;Acc:4856]

Sequence

>retro_cjac_338
ATGTCGGATTACGGCCTGCCCCAGTACAAGAGCGGGGACTTGGTGTTTGCCAAGTTGAAGGGCTATGCCCACTGGCCGGC
GCGAATAGAGCACATGACCCAGCCCAACCGTTACCAGGTGTTTTTCTTCGGAACCCACGAGACGGCCTTCCTGAGCCCCA
AACGCCTGTTCCCGTACAAGGAGTCCAAGGAGAAGTTCGGCAAGCCCAACAAGAGGCGCGGTTTCCGCGAGGGGCTGTGG
GAGATAGAGAACAACCCCACAGTCCAGGCCTCCGACTGCGTTTTCGCCCCGGAGATGGGCGGTGGAGACGGGCCCCGGCC
GGAGCCCGAGGCCGCAGAGAGCGACGCGGACAAGCCGAACCACGCCGAGGGCGGCGGCGACGAACCAAGGATGCCGGACG
ACGACGAGCCCGCCGAGGAGGAGAAGGGGCCGCTGAAGAGGAGCGCGGGGGACCCGCCTGATGACGCCCCCAAACGGCCC
AAGAAGGCCGACCCCGACCAGGAGGAGGAG

Alignment

ORF - retro_cjac_338 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.23 %
• Parental protein coverage: 53.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NKYQVFFFGTHETAFLGPKDLFPYEESKEKFGKPNKRKGFSEGLWEIENNPTVKASGYQSSQKKSCVEEP
          N.YQVFFFGTHETAFL.PK.LFPY.ESKEKFGKPNKR.GF.EGLWEIENNPTV.AS.............P
Retrocopy NRYQVFFFGTHETAFLSPKRLFPYKESKEKFGKPNKRRGFREGLWEIENNPTVQASDCVFAPEMGGGDGP

Parental  EPEPEATEGDSDKKGNAEGSSDEEGKLVIDEPAKEKNEKGALKRRAGDLLEDSPKRPKEAENPEEEE
          .PEPEA.E.D.DK...AEG..DE......DEPA.E..EKG.LKR.AGD...D.PKRPK.A....EEE
Retrocopy RPEPEAAESDADKPNHAEGGGDEPRMPDDDEPAEE--EKGPLKRSAGDPPDDAPKRPKKADPDQEEE

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	60.46 RPM
SRP051959_heart	0.00 RPM	26.87 RPM
SRP051959_kidney	0.00 RPM	60.72 RPM
SRP051959_liver	0.00 RPM	42.84 RPM
SRP051959_lung	0.00 RPM	29.12 RPM
SRP051959_lymph_node	0.00 RPM	21.30 RPM
SRP051959_skeletal_muscle	0.00 RPM	41.54 RPM
SRP051959_spleen	0.00 RPM	26.95 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_338 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_338 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_338 has 6 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_33
Pan troglodytes	retro_ptro_1
Pongo abelii	retro_pabe_6
Bos taurus	retro_btau_216
Sus scrofa	retro_sscr_65
Equus caballus	retro_ecab_5

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000039793	1 retrocopy	retro_btau_216,
Callithrix jacchus	ENSCJAG00000006157	2 retrocopies	retro_cjac_338 , retro_cjac_4022,
Callithrix jacchus	ENSCJAG00000012471	1 retrocopy	retro_cjac_4069,
Callithrix jacchus	ENSCJAG00000015775	1 retrocopy	retro_cjac_4165,
Dasypus novemcinctus	ENSDNOG00000010231	1 retrocopy	retro_dnov_4,
Equus caballus	ENSECAG00000011178	1 retrocopy	retro_ecab_5,
Echinops telfairi	ENSETEG00000005243	1 retrocopy	retro_etel_1899,
Homo sapiens	ENSG00000143321	1 retrocopy	retro_hsap_33,
Myotis lucifugus	ENSMLUG00000010413	1 retrocopy	retro_mluc_257,
Mus musculus	ENSMUSG00000004897	1 retrocopy	retro_mmus_3647,
Pongo abelii	ENSPPYG00000000703	1 retrocopy	retro_pabe_6,
Pan troglodytes	ENSPTRG00000001474	1 retrocopy	retro_ptro_1,
Sus scrofa	ENSSSCG00000006468	1 retrocopy	retro_sscr_65,