RetrogeneDB ID: retro_ptro_3047

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: GL392075.1:3416322..3416719(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FABP3
• Ensembl ID: ENSPTRG00000000457
• Aliases: None
• Description: None

Sequence

>retro_ptro_3047
ATGGTAGATGCCTTCCTGTGCACCTGGAAGCTCTCAGACAGCAAGAATTTTGATGACTACATGAAGTTAATCGGTGCAAG
TTTTGCTATCAGGCAGGTGGCTAGCATGACAAAGCCTACCACAATCATCAAAAAGAATGGGGACATTATCACCTTAAAAA
CACAGAGCATGTTCAAGAACACAGAGATCAGCTTTAAGCTGGGGATGGGGTTCGATGAGACAACAGCAGATGACAAAAAA
GGTCAAGTCCATTGTGACACTGGATGGAAGCAAACTTGTTCACCTGCAGAAGTGTAACGGGCAAGAGAGGACACTTGTGC
CAGAGCTAAGTGATGGGAAACTCATCCTGACACTCACCCAGGGCACTGCGGTTTACACTTGCACTTATGAGAAAGAG

Alignment

ORF - retro_ptro_3047 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.95 %
• Parental protein coverage: 99.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MVDAFLGTWKLVDSKNFDDYMKSLGVGFATRQVASMTKPTTIIEKNGDILTLKTHSTFKNTEISFKLGVE
          MVDAFL.TWKL.DSKNFDDYMK..G..FA.RQVASMTKPTTII.KNGDI.TLKT.S.FKNTEISFKLG..
Retrocopy MVDAFLCTWKLSDSKNFDDYMKLIGASFAIRQVASMTKPTTIIKKNGDIITLKTQSMFKNTEISFKLGMG

Parental  FDETTADD-RKVKSIVTLDGGKLVHLQKWDGQETTLVRELIDGKLILTLTHGTAVCTRTYEKE
          FDETTADD..KVKSIVTLDG.KLVHLQK..GQE.TLV.EL.DGKLILTLT.GTAV.T.TYEKE
Retrocopy FDETTADD>KKVKSIVTLDGSKLVHLQKCNGQERTLVPELSDGKLILTLTQGTAVYTCTYEKE

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	58.16 RPM
SRP007412_cerebellum	0.00 RPM	7.67 RPM
SRP007412_heart	0.00 RPM	927.05 RPM
SRP007412_kidney	0.00 RPM	330.69 RPM
SRP007412_liver	0.00 RPM	6.32 RPM
SRP007412_testis	0.00 RPM	5.16 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3047 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3047 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3047 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1258
Gorilla gorilla	retro_ggor_990
Pongo abelii	retro_pabe_1048
Macaca mulatta	retro_mmul_1311

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 48 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016819	2 retrocopies	retro_btau_1467, retro_btau_295,
Danio rerio	ENSDARG00000023290	1 retrocopy	retro_drer_33,
Dasypus novemcinctus	ENSDNOG00000000511	2 retrocopies	retro_dnov_1510, retro_dnov_2482,
Equus caballus	ENSECAG00000024852	1 retrocopy	retro_ecab_519,
Homo sapiens	ENSG00000121769	1 retrocopy	retro_hsap_1258,
Gorilla gorilla	ENSGGOG00000014432	1 retrocopy	retro_ggor_990,
Macropus eugenii	ENSMEUG00000012501	6 retrocopies	retro_meug_1037, retro_meug_148, retro_meug_1660, retro_meug_273, retro_meug_563, retro_meug_819,
Microcebus murinus	ENSMICG00000009359	4 retrocopies	retro_mmur_1490, retro_mmur_203, retro_mmur_621, retro_mmur_734,
Myotis lucifugus	ENSMLUG00000013609	2 retrocopies	retro_mluc_1144, retro_mluc_1717,
Mus musculus	ENSMUSG00000028773	3 retrocopies	retro_mmus_2804, retro_mmus_3204, retro_mmus_65,
Nomascus leucogenys	ENSNLEG00000001586	1 retrocopy	retro_nleu_2097,
Otolemur garnettii	ENSOGAG00000013757	4 retrocopies	retro_ogar_1148, retro_ogar_1312, retro_ogar_1873, retro_ogar_959,
Pongo abelii	ENSPPYG00000001616	1 retrocopy	retro_pabe_1048,
Pan troglodytes	ENSPTRG00000000457	1 retrocopy	retro_ptro_3047 ,
Pan troglodytes	ENSPTRG00000018564	1 retrocopy	retro_ptro_402,
Pan troglodytes	ENSPTRG00000020373	12 retrocopies	retro_ptro_1029, retro_ptro_1030, retro_ptro_1498, retro_ptro_1654, retro_ptro_2029, retro_ptro_2131, retro_ptro_2265, retro_ptro_2295, retro_ptro_2664, retro_ptro_3135, retro_ptro_823, retro_ptro_875,
Pan troglodytes	ENSPTRG00000022654	1 retrocopy	retro_ptro_2493,
Rattus norvegicus	ENSRNOG00000012879	1 retrocopy	retro_rnor_2199,
Ictidomys tridecemlineatus	ENSSTOG00000003842	3 retrocopies	retro_itri_1544, retro_itri_640, retro_itri_641,