RetrogeneDB ID: retro_cjac_2227

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:33137293..33137613(-)
• Located in intron of: ENSCJAG00000001403

Retrocopy information

• Ensembl ID: ENSCJAG00000032624
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FABP5
• Ensembl ID: ENSCJAG00000000444
• Aliases: None
• Description: fatty acid binding protein 5 (psoriasis-associated) [Source:HGNC Symbol;Acc:3560]

Sequence

>retro_cjac_2227
GGAATGAGAATAGCTTTGAGAAAAATGGGCACAACGGCCAAACCAGAGTTATCATCATTTGTGATGGCAAAAACCTCACC
ATAAAAACTGAGCACTTAGACAACAGCAGAGTTTTCTCTCTAGGAGAGAAGTTTGAAGAAACTATAGCTCATGACAGAAA
AACTCAGACTGTCTGCAACCTTGCAGATGGAGCATTGGTTCAGCATCAGGAGTGGGATGGGAAGAAAAGAACAATAACAA
GAAAATTGAAAGATAGAACATTTGTGGTAGTCTGTGTCATGAACAATGTCACCTGTTCTCGGATCTATAAAAAGGTAGAG

Alignment

ORF - retro_cjac_2227 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.82 %
• Parental protein coverage: 81.34 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GVGIALRKMGAMAKPDC-IITCDGKNLTIKTESTLKTTQFSCTLGEKFEETTADGRKTQTVCNFTDGALV
          G..IALRKMG..AKP...II.CDGKNLTIKTE.......FS..LGEKFEET.A..RKTQTVCN..DGALV
Retrocopy GMRIALRKMGTTAKPEL<IIICDGKNLTIKTEHLDNSRVFS--LGEKFEETIAHDRKTQTVCNLADGALV

Parental  QHQEWDGKESTITRKLKDGKLVVDCVINNVTCTRIYEKVE
          QHQEWDGK..TITRKLKD...VV.CV.NNVTC.RIY.KVE
Retrocopy QHQEWDGKKRTITRKLKDRTFVVVCVMNNVTCSRIYKKVE

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
SRP051959_colon	0.07 RPM	4.68 RPM
SRP051959_heart	0.12 RPM	17.70 RPM
SRP051959_kidney	0.00 RPM	1.15 RPM
SRP051959_liver	0.00 RPM	0.95 RPM
SRP051959_lung	0.07 RPM	17.50 RPM
SRP051959_lymph_node	0.00 RPM	7.28 RPM
SRP051959_skeletal_muscle	0.02 RPM	7.23 RPM
SRP051959_spleen	0.00 RPM	12.02 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2227 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2227 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2227 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3000
Pan troglodytes	retro_ptro_2029
Gorilla gorilla	retro_ggor_2079
Macaca mulatta	retro_mmul_1920

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Parental genes homology:

Parental genes homology involve 28 parental genes, and 114 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	ENSCJAG00000000433	1 retrocopy	retro_cjac_2486,
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,
Gorilla gorilla	ENSGGOG00000005964	8 retrocopies	retro_ggor_1005, retro_ggor_1163, retro_ggor_2079, retro_ggor_2276, retro_ggor_2284, retro_ggor_2563, retro_ggor_2931, retro_ggor_940,
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	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,
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,