RetrogeneDB ID: retro_cjac_3177

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:6502821..6503245(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000021603
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: POMP
• Ensembl ID: ENSCJAG00000019473
• Aliases: None
• Description: proteasome maturation protein [Source:HGNC Symbol;Acc:20330]

Sequence

>retro_cjac_3177
ATGAATGCCAGAGGACTTGGATCTGAGCTAAAGGACAGTATTCCAGGTACAGAGCTTTCAGCAAGTGGACCTTTTGAAAG
TCATGATCTTCTTCGGAAGGGTTTTTCTTGTGTGAAAAATGAACTTTTGCCTAGTCATCCTCTCGAATTATCAGAAAAAA
AATTTCCAGCTCAACCAAGATAAAATGAATTTTTCCACTCTGAGAAACATTCAGGGTCTGTTTGCTCCACTAAAATTACA
GATGGAATTCAAGGCAGTGCAGCAGGTTCAGCATCTTCCATTTCTTCCAAGCTCAAATCTTTCACTGGATATTTTGAGGG
GTAATGATGAGACTATTGGATTTGAGGATATTCTCAATGATCCATCACAAAGCGAAGTCATGGGAGAGCCACACTTGATG
GTGGAATATAAACTGGGTTTACTA

Alignment

ORF - retro_cjac_3177 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.89 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MNARGLGSELKDSIPVTELSASGPFESHDLLRKGFSCVKNELLPSHPLELSEK-NFQLNQDKMNFSTLRN
          MNARGLGSELKDSIP.TELSASGPFESHDLLRKGFSCVKNELLPSHPLELSEK.NFQLNQDKMNFSTLRN
Retrocopy MNARGLGSELKDSIPGTELSASGPFESHDLLRKGFSCVKNELLPSHPLELSEK>NFQLNQDKMNFSTLRN

Parental  IQGLFAPLKLQMEFKAVQQVQRLPFLPSSNLSLDILRGNDETIGFEDILNDPSQSEVMGEPHLMVEYKLG
          IQGLFAPLKLQMEFKAVQQVQ.LPFLPSSNLSLDILRGNDETIGFEDILNDPSQSEVMGEPHLMVEYKLG
Retrocopy IQGLFAPLKLQMEFKAVQQVQHLPFLPSSNLSLDILRGNDETIGFEDILNDPSQSEVMGEPHLMVEYKLG

Parental  LL
          LL
Retrocopy LL

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	0.18 RPM	27.96 RPM
SRP051959_heart	0.16 RPM	20.59 RPM
SRP051959_kidney	0.16 RPM	20.41 RPM
SRP051959_liver	0.32 RPM	25.47 RPM
SRP051959_lung	0.10 RPM	18.41 RPM
SRP051959_lymph_node	0.14 RPM	17.12 RPM
SRP051959_skeletal_muscle	0.33 RPM	34.39 RPM
SRP051959_spleen	0.29 RPM	23.26 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3177 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3177 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3177 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 34 parental genes, and 100 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000009671	1 retrocopy	retro_acar_56,
Ailuropoda melanoleuca	ENSAMEG00000008961	1 retrocopy	retro_amel_965,
Bos taurus	ENSBTAG00000014024	3 retrocopies	retro_btau_1392, retro_btau_1563, retro_btau_755,
Choloepus hoffmanni	ENSCHOG00000012807	12 retrocopies	retro_chof_1473, retro_chof_1715, retro_chof_1767, retro_chof_2191, retro_chof_2256, retro_chof_2360, retro_chof_2479, retro_chof_442, retro_chof_658, retro_chof_738, retro_chof_739, retro_chof_924,
Callithrix jacchus	ENSCJAG00000019473	3 retrocopies	retro_cjac_2947, retro_cjac_3177 , retro_cjac_4191,
Cavia porcellus	ENSCPOG00000001710	3 retrocopies	retro_cpor_1465, retro_cpor_411, retro_cpor_630,
Dasypus novemcinctus	ENSDNOG00000008848	4 retrocopies	retro_dnov_1744, retro_dnov_1919, retro_dnov_2264, retro_dnov_2301,
Equus caballus	ENSECAG00000011951	1 retrocopy	retro_ecab_329,
Echinops telfairi	ENSETEG00000012448	2 retrocopies	retro_etel_1043, retro_etel_718,
Felis catus	ENSFCAG00000008235	5 retrocopies	retro_fcat_2020, retro_fcat_266, retro_fcat_525, retro_fcat_742, retro_fcat_834,
Homo sapiens	ENSG00000132963	2 retrocopies	retro_hsap_2261, retro_hsap_4866,
Gorilla gorilla	ENSGGOG00000015316	2 retrocopies	retro_ggor_1684, retro_ggor_3038,
Loxodonta africana	ENSLAFG00000003665	1 retrocopy	retro_lafr_1113,
Macropus eugenii	ENSMEUG00000015416	2 retrocopies	retro_meug_1570, retro_meug_1571,
Myotis lucifugus	ENSMLUG00000010322	1 retrocopy	retro_mluc_53,
Macaca mulatta	ENSMMUG00000000097	2 retrocopies	retro_mmul_1027, retro_mmul_2603,
Mustela putorius furo	ENSMPUG00000004690	3 retrocopies	retro_mputfur_1023, retro_mputfur_1447, retro_mputfur_366,
Mus musculus	ENSMUSG00000029649	3 retrocopies	retro_mmus_1417, retro_mmus_2356, retro_mmus_3300,
Nomascus leucogenys	ENSNLEG00000000572	3 retrocopies	retro_nleu_1285, retro_nleu_1440, retro_nleu_1998,
Oryctolagus cuniculus	ENSOCUG00000010137	1 retrocopy	retro_ocun_1377,
Otolemur garnettii	ENSOGAG00000006044	1 retrocopy	retro_ogar_1672,
Ochotona princeps	ENSOPRG00000016517	2 retrocopies	retro_opri_459, retro_opri_833,
Procavia capensis	ENSPCAG00000009680	1 retrocopy	retro_pcap_178,
Pongo abelii	ENSPPYG00000005247	1 retrocopy	retro_pabe_3783,
Pan troglodytes	ENSPTRG00000005745	1 retrocopy	retro_ptro_1601,
Pteropus vampyrus	ENSPVAG00000000032	3 retrocopies	retro_pvam_262, retro_pvam_551, retro_pvam_813,
Rattus norvegicus	ENSRNOG00000048470	2 retrocopies	retro_rnor_1289, retro_rnor_2020,
Rattus norvegicus	ENSRNOG00000049229	4 retrocopies	retro_rnor_1590, retro_rnor_1843, retro_rnor_2325, retro_rnor_625,
Sorex araneus	ENSSARG00000001134	5 retrocopies	retro_sara_184, retro_sara_371, retro_sara_423, retro_sara_57, retro_sara_64,
Ictidomys tridecemlineatus	ENSSTOG00000013687	2 retrocopies	retro_itri_1612, retro_itri_614,
Tupaia belangeri	ENSTBEG00000012149	13 retrocopies	retro_tbel_1015, retro_tbel_1278, retro_tbel_193, retro_tbel_2264, retro_tbel_3135, retro_tbel_3412, retro_tbel_3437, retro_tbel_346, retro_tbel_3491, retro_tbel_3861, retro_tbel_4172, retro_tbel_4342, retro_tbel_4708,
Tarsius syrichta	ENSTSYG00000005121	4 retrocopies	retro_tsyr_1002, retro_tsyr_1693, retro_tsyr_1887, retro_tsyr_1984,
Tursiops truncatus	ENSTTRG00000012924	4 retrocopies	retro_ttru_1166, retro_ttru_1465, retro_ttru_374, retro_ttru_577,
Vicugna pacos	ENSVPAG00000001315	2 retrocopies	retro_vpac_266, retro_vpac_284,