RetrogeneDB ID: retro_ptro_2029

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:162125312..162125693(+)
• Located in intron of: ENSPTRG00000016556

Retrocopy information

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

Parental gene information

• Parental gene symbol: FABP5
• Ensembl ID: ENSPTRG00000020373
• Aliases: FABP5, FABP5L2, FABP5L7
• Description: fatty acid binding protein 5 (psoriasis-associated) [Source:HGNC Symbol;Acc:3560]

Sequence

>retro_ptro_2029
GGAAGATGATGCCTAGTGGACAGCAAAGGCCTTGATGAATACGTGAAGGAACTAGGAGTGGGAATAGCTTTGTGAAAAAT
GGGCACAATGGCCAAGCCAGAGTGTATCATCATTTGTGATGACAAAAACCTCACCATAAAAACTCAGAGCACTTAGAAAA
CAGCACAGTTTTCTTGTACCCTGGGAGAGAAGGTTGAAGAAACTACAGCTCATAGCAAAAAAACTCAGACTCTCTACAAC
TTTACAGATGGATCATTGGTTCAGCATCAGGAGTGGGATGGGAAGAAAAGCACAATAACAAGAAAATTGAAAGATGGGAA
ATTCATGGTAGACTGTGTCATGAACAATGTCACCTGTTCTCAGATCTATAAAAAAGTAGAA

Alignment

ORF - retro_ptro_2029 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.53 %
• Parental protein coverage: 94.07 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GRWRLVDSKGFDEYMKELGVGIALRKMGAMAKPDCIITCDGKNLTIKTESTLKTTQFSCTLGEKFEETTA
          GR..LVDSKG.DEY.KELGVGIAL.KMG.MAKP.CII.CD.KNLTIKT.ST.KT.QFSCTLGEK.EETTA
Retrocopy GR*CLVDSKGLDEYVKELGVGIAL*KMGTMAKPECIIICDDKNLTIKTQST*KTAQFSCTLGEKVEETTA

Parental  DGRKTQTVCNFTDGALVQHQEWDGKESTITRKLKDGKLVVECVMNNVTCTRIYEKVE
          ...KTQT..NFTDG.LVQHQEWDGK.STITRKLKDGK..V.CVMNNVTC..IY.KVE
Retrocopy HSKKTQTLYNFTDGSLVQHQEWDGKKSTITRKLKDGKFMVDCVMNNVTCSQIYKKVE

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	16.25 RPM
SRP007412_cerebellum	0.04 RPM	8.64 RPM
SRP007412_heart	0.00 RPM	19.18 RPM
SRP007412_kidney	0.00 RPM	0.76 RPM
SRP007412_liver	0.00 RPM	1.18 RPM
SRP007412_testis	0.00 RPM	20.87 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2029 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2029 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2029 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3000
Gorilla gorilla	retro_ggor_2079
Macaca mulatta	retro_mmul_1920
Callithrix jacchus	retro_cjac_2227

---

Parental genes homology:

Parental genes homology involve 29 parental genes, and 108 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014619	1 retrocopy	retro_amel_1139,
Bos taurus	ENSBTAG00000047330	3 retrocopies	retro_btau_1312, retro_btau_1828, retro_btau_886,
Callithrix jacchus	ENSCJAG00000000444	4 retrocopies	retro_cjac_1832, retro_cjac_2227, retro_cjac_2816, retro_cjac_4084,
Cavia porcellus	ENSCPOG00000025732	1 retrocopy	retro_cpor_948,
Dasypus novemcinctus	ENSDNOG00000018066	5 retrocopies	retro_dnov_1073, retro_dnov_1231, retro_dnov_1318, retro_dnov_2392, retro_dnov_559,
Equus caballus	ENSECAG00000008270	2 retrocopies	retro_ecab_894, retro_ecab_938,
Erinaceus europaeus	ENSEEUG00000014023	2 retrocopies	retro_eeur_405, retro_eeur_627,
Echinops telfairi	ENSETEG00000007443	14 retrocopies	retro_etel_1024, retro_etel_1241, retro_etel_1276, retro_etel_1405, retro_etel_1467, retro_etel_1706, retro_etel_1842, retro_etel_1904, retro_etel_2003, retro_etel_512, retro_etel_602, retro_etel_620, retro_etel_806, retro_etel_994,
Felis catus	ENSFCAG00000006032	2 retrocopies	retro_fcat_1243, retro_fcat_1834,
Homo sapiens	ENSG00000164687	12 retrocopies	retro_hsap_1205, retro_hsap_1279, retro_hsap_1520, retro_hsap_1521, retro_hsap_2167, retro_hsap_2568, retro_hsap_3000, retro_hsap_3357, retro_hsap_3376, retro_hsap_3811, retro_hsap_4717, retro_hsap_880,
Latimeria chalumnae	ENSLACG00000008511	3 retrocopies	retro_lcha_37, retro_lcha_45, retro_lcha_57,
Macropus eugenii	ENSMEUG00000002136	1 retrocopy	retro_meug_1874,
Microcebus murinus	ENSMICG00000001311	2 retrocopies	retro_mmur_137, retro_mmur_702,
Myotis lucifugus	ENSMLUG00000009514	3 retrocopies	retro_mluc_1590, retro_mluc_1920, retro_mluc_501,
Macaca mulatta	ENSMMUG00000000486	4 retrocopies	retro_mmul_1417, retro_mmul_1920, retro_mmul_2095, retro_mmul_2230,
Mus musculus	ENSMUSG00000027533	4 retrocopies	retro_mmus_1685, retro_mmus_1791, retro_mmus_2084, retro_mmus_3185,
Otolemur garnettii	ENSOGAG00000002413	10 retrocopies	retro_ogar_1024, retro_ogar_1151, retro_ogar_1286, retro_ogar_1676, retro_ogar_2873, retro_ogar_3066, retro_ogar_3099, retro_ogar_3265, retro_ogar_715, retro_ogar_878,
Oryzias latipes	ENSORLG00000008282	1 retrocopy	retro_olat_7,
Pongo abelii	ENSPPYG00000018699	1 retrocopy	retro_pabe_27,
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,
Pteropus vampyrus	ENSPVAG00000017850	5 retrocopies	retro_pvam_1159, retro_pvam_467, retro_pvam_531, retro_pvam_852, retro_pvam_89,
Rattus norvegicus	ENSRNOG00000049075	3 retrocopies	retro_rnor_1762, retro_rnor_1879, retro_rnor_1997,
Sus scrofa	ENSSSCG00000006153	1 retrocopy	retro_sscr_476,
Ictidomys tridecemlineatus	ENSSTOG00000007877	3 retrocopies	retro_itri_1305, retro_itri_389, retro_itri_72,
Tarsius syrichta	ENSTSYG00000001472	5 retrocopies	retro_tsyr_126, retro_tsyr_1534, retro_tsyr_1894, retro_tsyr_1982, retro_tsyr_2024,
Tursiops truncatus	ENSTTRG00000005377	1 retrocopy	retro_ttru_1800,