RetrogeneDB ID: retro_pabe_6

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:23495671..23496400(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000016274
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: HDGF
• Ensembl ID: ENSPPYG00000000703
• Aliases: None
• Description: hepatoma-derived growth factor [Source:HGNC Symbol;Acc:4856]

Sequence

>retro_pabe_6
ATGTCGGCCTACGGCATGCCCATGTACAAGAGCGGGGACCTGGTGTTTGCCAAGTTAAAGGGCTATGCCCACTGGCCGGC
GAGGATAGAGCACATGACCCAGCCCAACCGCTACCAGGTGTTTTTCTTCGGGACCCACGAAACGGCCTTCCTGAGTCCCA
AACGCCTGTTCCCGTACAAGGAGTGCAAGGAGAAGTTCGGCAAGCCCAACAAGAGGCGCGGCTTCAGCGAGGGGCTGTGG
GAGATCGAGAACAATCCCACGGTCCAGGCCTCCGACTGCCCATTAGCCTCAGAGAAGGGCAGCGGAGACGGGCCTTGGCC
GGAGCCCGAGGGCGACGAGGACAAGCCGACCCACGCTGATGGCGGCGGCGACGAATTGGGGAAGCCGGACGACGACAAGC
CCACTGAGGAGGAGAAGGAGAAGGGGTCGCTGAAGAGGAGCGCGGGGGACCCGCCGGAGGACGCCCCCAAACGACCCAAG
GAGGCAGGCCCCGACCAAGAGGAGAAGGAGGAGGCGGAGGCGGCGGCGGCGGCGGCGGCGGCCGTCGACGAGGAGAGTCC
GCTCCTCGTGGCGGTGGAGAACGGCAGCGCCCCTAGCGAGCCCGGCCTGGCCTGCGAGCCGCCTCAGCCAGAGGAGGAGG
AGCTCCGGGAGGAAGAAGTCGCCGACGAGGAGGCCTCCCAGGAGTGGCATTCCGAGGCACCGGGCGGCGGAGATCGCGAC
AGCCTGTAG

Alignment

ORF - retro_pabe_6 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.25 %
• Parental protein coverage: 58.75 %
• 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  EPEPEATEGDGDKKGNAEGSSDEEGKLVIDEPAKEKNEKGALKRRAGDLLEDSPKRPKEAENPEGEEKEA
          .PEPE...GD.DK...A.G..DE.GK...D.P..E..EKG.LKR.AGD..ED.PKRPKEA..P..EEKE.
Retrocopy WPEPE---GDEDKPTHADGGGDELGKPDDDKPTEEEKEKGSLKRSAGDPPEDAPKRPKEA-GPDQEEKEE

Parental  A
          A
Retrocopy A

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	0.00 RPM	98.64 RPM
SRP007412_cerebellum	0.00 RPM	132.06 RPM
SRP007412_heart	0.00 RPM	51.75 RPM
SRP007412_kidney	0.00 RPM	195.37 RPM
SRP007412_liver	0.03 RPM	83.02 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_6 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_6 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_6 has 6 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_33
Pan troglodytes	retro_ptro_1
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 11 parental genes, and 12 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,
Sus scrofa	ENSSSCG00000006468	1 retrocopy	retro_sscr_65,