RetrogeneDB ID: retro_pabe_1048

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 13:42361815..42362211(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FABP3
• Ensembl ID: ENSPPYG00000001616
• Aliases: None
• Description: fatty acid binding protein 3, muscle and heart (mammary-derived growth inhibitor) [Source:HGNC Symbol;Acc:3557]

Sequence

>retro_pabe_1048
ATGGTAGATGCCTTCCTGTGCACCTGGAAGCTCTCAGACAGCAAGAATTTTGATGACTACATGAAGTTAATCGGTGCAAG
TTTTGCTACCAGGCAAGTGGCTAGCGTGACAAAGCCTACCACAGTCATCAAAAAGAATGGGGACATTATCACCTTAAAAA
CACAGAGCATGTTCAAGAACACAGAGATCAGCTTTAAGCTGGGGATGGAGTTCGATGAGACAACAGCAGATGACAAAAAG
GTCAAGTCCATTGTGACACTGGATGGAGGCAAACTTGTTCACCTGCAGAAGTGTAACGGGCAAGAGAGGACATTTGTGTC
AGAGCTAAGTGATGGGAAACTCATCCTGACACTCACCCAGGGCACTGCGGTTTACACTCGCACTTATGAGAAAGAG

Alignment

ORF - retro_pabe_1048 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.33 %
• Parental protein coverage: 99.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVDAFLGTWKLVDSKNFDDYMKSLGVGFATRQVASMTKPTTIIEKNGDILTLKTHSTFKNTEISFKLGVE
          MVDAFL.TWKL.DSKNFDDYMK..G..FATRQVAS.TKPTT.I.KNGDI.TLKT.S.FKNTEISFKLG.E
Retrocopy MVDAFLCTWKLSDSKNFDDYMKLIGASFATRQVASVTKPTTVIKKNGDIITLKTQSMFKNTEISFKLGME

Parental  FDETTADDRKVKSIVTLDGGKLVHLQKWDGQETTLVRELIDGKLILTLTHGTAVCTRTYEKE
          FDETTADD.KVKSIVTLDGGKLVHLQK..GQE.T.V.EL.DGKLILTLT.GTAV.TRTYEKE
Retrocopy FDETTADDKKVKSIVTLDGGKLVHLQKCNGQERTFVSELSDGKLILTLTQGTAVYTRTYEKE

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	106.82 RPM
SRP007412_cerebellum	0.00 RPM	44.26 RPM
SRP007412_heart	0.03 RPM	1415.50 RPM
SRP007412_kidney	0.00 RPM	152.51 RPM
SRP007412_liver	0.00 RPM	6.79 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1048 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1048 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1048 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1258
Pan troglodytes	retro_ptro_3047
Gorilla gorilla	retro_ggor_990
Macaca mulatta	retro_mmul_1311

---

Parental genes homology:

Parental genes homology involve 19 parental genes, and 37 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 ,
Pongo abelii	ENSPPYG00000016979	1 retrocopy	retro_pabe_213,
Pongo abelii	ENSPPYG00000018699	1 retrocopy	retro_pabe_27,
Pongo abelii	ENSPPYG00000018703	1 retrocopy	retro_pabe_3016,
Pan troglodytes	ENSPTRG00000000457	1 retrocopy	retro_ptro_3047,
Rattus norvegicus	ENSRNOG00000012879	1 retrocopy	retro_rnor_2199,
Ictidomys tridecemlineatus	ENSSTOG00000003842	3 retrocopies	retro_itri_1544, retro_itri_640, retro_itri_641,