RetrogeneDB ID: retro_ptro_1

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:22791790..22792540(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000017769
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: HDGF
• Ensembl ID: ENSPTRG00000001474
• Aliases: None
• Description: None

Sequence

>retro_ptro_1
ATGTCGGACTACAGCATGCCCACGTACAAGAGCGGGGACCTGGTGTTTGCCAAGTTAAAGGGCTATGCCCACTGGCCGGC
GAGGATAGAGGACATGACCCAGCCCAACCGCTACCAGGTGTTTTTCTTCGGGACCCACGAGACGGCCTTCCTGAGTCCCA
AACGCCTGTTCCCGTACAAGGAGTGCAAGGAGAAGTTCGGCAAGCCCAACAAGAGGCGCGGCTTCAGCGAGGGGCTGTGG
GAAATCGAGAACAACCCCACGGTCCAGGCCTCCGACTGCCCATTAGCCTCAGAGAAGGGCAGCGGAGACGGGCCTTGGCC
GGAGCCCGAGGCCGCGGAGGGCGACGAGGACAAGCCGACCCACGCTGGTGGCGGCGGCGACGAATTGGGGAAGCCGGACG
ACGACAAGCCCACTGAGGAGGAGAAGGGGCCGCTGAAGAGGAGCGCGGGGGACCCGCCGGAGGACGCCCCCAAACGACCC
AAGAAGGCAGCCCCCGACCAAGAGGAGAAGGAGGAGGCGGAGGCGGAGAGGGCGGCGGCGGCGATGGCGGCGGCGGCGGC
GGCCGTCGACGAGGAGTGTCCGTTCCTTGTGGCGGTGGAGAACGGCAGCGCCCCTAGCGAGCCGGGCCTGGCCTGCGAGC
CGCCTCAGCCAGAGGAGGAGGAGCTCCGGGAGGAAGAAGTCGCGGACGAGGAGGCCTCCCAGGAGTGGCATGCCGAGGCA
CCGGGCGGCGGAGATCGCGACAGCCTGTAG

Alignment

ORF - retro_ptro_1 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.97 %
• Parental protein coverage: 56.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NKYQVFFFGTHETAFLGPKDLFPYEESKEKFGKPNKRKGFSEGLWEIENNPTVKASGYQSSQKKSCVEEP
          N.YQVFFFGTHETAFL.PK.LFPY.E.KEKFGKPNKR.GFSEGLWEIENNPTV.AS.......K.....P
Retrocopy NRYQVFFFGTHETAFLSPKRLFPYKECKEKFGKPNKRRGFSEGLWEIENNPTVQASDCPLASEKGSGDGP

Parental  EPEPEAAEGDGDKKGNAEGSSDEEGKLVIDEPAKEKNEKGALKRRAGDLLEDSPKRPKEAENPEGEEKEA
          .PEPEAAEGD.DK...A.G..DE.GK...D.P..E..EKG.LKR.AGD..ED.PKRPK.A..P..EEKE.
Retrocopy WPEPEAAEGDEDKPTHAGGGGDELGKPDDDKPTEE--EKGPLKRSAGDPPEDAPKRPKKAA-PDQEEKEE

Parental  ATLE
          A..E
Retrocopy AEAE

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
SRP007412_brain_prefrontal_cortex	0.30 RPM	86.44 RPM
SRP007412_cerebellum	0.72 RPM	148.59 RPM
SRP007412_heart	0.09 RPM	102.01 RPM
SRP007412_kidney	0.73 RPM	255.56 RPM
SRP007412_liver	0.49 RPM	240.01 RPM
SRP007412_testis	46.47 RPM	46.16 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1 has 6 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_33
Pongo abelii	retro_pabe_6
Callithrix jacchus	retro_cjac_338
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 12 parental genes, and 13 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,
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 ,
Pan troglodytes	ENSPTRG00000020786	1 retrocopy	retro_ptro_2811,
Sus scrofa	ENSSSCG00000006468	1 retrocopy	retro_sscr_65,