RetrogeneDB ID: retro_cjac_1410

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 15:70945027..70945587(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PEBP1
• Ensembl ID: ENSCJAG00000009314
• Aliases: None
• Description: phosphatidylethanolamine binding protein 1 [Source:HGNC Symbol;Acc:8630]

Sequence

>retro_cjac_1410
ATGCCAGTGGACCTCAGCAAGTGGTCTGGCCCTTGAGCCTGCAGGAAGTGGACGAGCAGCTGCAGCACCCGCTGCATGTC
ACCTATGCTGGGGCAGTGATGCGTGAGCTGGGCAAAGTGCTAATGTCCACCCAGGTTAAGAACACACCCACCAGCGTTTT
GTAGGGTGCTCTTGATTCGGAGAAACTCTGCACCTTGGTCCTGACAGACTCAGGTGGTCCCAGCAGAAAGGACCCCAAAT
ATAGGGAATGGTATCATTTCCTGGTGGTCAACATGAAGGGTAATGACATCAGCAGAGGTACAGTCCTCTCCAATTACCTG
GGCTCAGGGCCTCCCAAGACCACGGGCCTCCACTGCTCTGTCTGGCTGGTTTACCAGCAGGACGGGTTGCTGAAGTCTGA
AGAGTCCATCCTCAGCAACTGACCTGGAGACCACTGTGGCAATTTCAAGGTGGCGTCCTTCTGTAAAAAGCACGAGCTCT
GGGCCCTGGTGGCCGGCACATCTTACCAGGCTGAGTGGGATGATTAAGTGCCTAAACTGTACAAGCAGCTGTCTGGGAAG

Alignment

ORF - retro_cjac_1410 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.6 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPVDLSKWSGP-LSLQEVDEQPQHPLHVTYGGAAVDELGKVLTPTQVKNRPTSISWDGLDSGKLYTLVLT
          MPVDLSKWSGP.LSLQEVDEQ.QHPLHVTY.GA...ELGKVL..TQVKN.PTS.....LDS.KL.TLVLT
Retrocopy MPVDLSKWSGP<LSLQEVDEQLQHPLHVTYAGAVMRELGKVLMSTQVKNTPTSVL*GALDSEKLCTLVLT

Parental  DPDAPSRKDPKYREWHHFLVVNMKGNDISSGTVLSDYVGSGPPKGTGLHRYVWLVYEQDRPLKCDEPILS
          D...PSRKDPKYREW.HFLVVNMKGNDIS.GTVLS.Y.GSGPPK.TGLH..VWLVY.QD..LK..E.ILS
Retrocopy DSGGPSRKDPKYREWYHFLVVNMKGNDISRGTVLSNYLGSGPPKTTGLHCSVWLVYQQDGLLKSEESILS

Parental  NRSGDHRGKFKVASFRKKYQLRAPVAGTCYQAEWDDYVPKLYEQLSGK
          N..GDH.G.FKVASF.KK..L.A.VAGT.YQAEWDD.VPKLY.QLSGK
Retrocopy N*PGDHCGNFKVASFCKKHELWALVAGTSYQAEWDD*VPKLYKQLSGK

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	0.00 RPM	37.74 RPM
SRP051959_heart	0.00 RPM	87.39 RPM
SRP051959_kidney	0.00 RPM	152.97 RPM
SRP051959_liver	0.00 RPM	147.57 RPM
SRP051959_lung	0.02 RPM	51.36 RPM
SRP051959_lymph_node	0.00 RPM	38.47 RPM
SRP051959_skeletal_muscle	0.00 RPM	77.50 RPM
SRP051959_spleen	0.00 RPM	48.99 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1410 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1410 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1410 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_328

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 52 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016143	2 retrocopies	retro_amel_1355, retro_amel_754,
Bos taurus	ENSBTAG00000018115	2 retrocopies	retro_btau_1183, retro_btau_705,
Canis familiaris	ENSCAFG00000009910	1 retrocopy	retro_cfam_526,
Callithrix jacchus	ENSCJAG00000009314	2 retrocopies	retro_cjac_1410 , retro_cjac_818,
Erinaceus europaeus	ENSEEUG00000003689	1 retrocopy	retro_eeur_292,
Felis catus	ENSFCAG00000002277	3 retrocopies	retro_fcat_1317, retro_fcat_1360, retro_fcat_299,
Homo sapiens	ENSG00000089220	3 retrocopies	retro_hsap_1456, retro_hsap_2288, retro_hsap_492,
Gorilla gorilla	ENSGGOG00000013281	3 retrocopies	retro_ggor_1121, retro_ggor_1701, retro_ggor_461,
Myotis lucifugus	ENSMLUG00000002259	7 retrocopies	retro_mluc_103, retro_mluc_1612, retro_mluc_1742, retro_mluc_2357, retro_mluc_2373, retro_mluc_984, retro_mluc_998,
Macaca mulatta	ENSMMUG00000005098	4 retrocopies	retro_mmul_1621, retro_mmul_2272, retro_mmul_328, retro_mmul_442,
Mustela putorius furo	ENSMPUG00000002861	3 retrocopies	retro_mputfur_1228, retro_mputfur_1361, retro_mputfur_223,
Mus musculus	ENSMUSG00000032959	4 retrocopies	retro_mmus_138, retro_mmus_1857, retro_mmus_2314, retro_mmus_542,
Nomascus leucogenys	ENSNLEG00000000322	1 retrocopy	retro_nleu_1966,
Oryctolagus cuniculus	ENSOCUG00000008395	2 retrocopies	retro_ocun_1329, retro_ocun_1900,
Otolemur garnettii	ENSOGAG00000001740	1 retrocopy	retro_ogar_2750,
Pongo abelii	ENSPPYG00000005011	2 retrocopies	retro_pabe_1202, retro_pabe_241,
Pan troglodytes	ENSPTRG00000005512	3 retrocopies	retro_ptro_1621, retro_ptro_371, retro_ptro_992,
Rattus norvegicus	ENSRNOG00000001136	3 retrocopies	retro_rnor_1223, retro_rnor_46, retro_rnor_541,
Ictidomys tridecemlineatus	ENSSTOG00000004085	2 retrocopies	retro_itri_1603, retro_itri_961,
Tupaia belangeri	ENSTBEG00000000177	2 retrocopies	retro_tbel_272, retro_tbel_2728,
Tursiops truncatus	ENSTTRG00000000658	1 retrocopy	retro_ttru_1164,