RetrogeneDB ID: retro_cjac_2002

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 20:1866134..1866494(-)
• Located in intron of: ENSCJAG00000012577

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBA52
• Ensembl ID: ENSCJAG00000007470
• Aliases: None
• Description: ubiquitin A-52 residue ribosomal protein fusion product 1 [Source:HGNC Symbol;Acc:12458]

Sequence

>retro_cjac_2002
ATGTGGATTTTTGTGAAGACCCTCACAGGCAAGACCACTGCCCTTGAGGTCGAGCCCAGGGACACCACTGCAAATGTCAA
AGCCAATATCCGAGACAACTAAGGCATCCTACCTGACCAGCAGTGTCTGATATTTGAGAGCAAACAGCTGGAGGATGGCC
ACACTCTCTTAGACTGCAACATTCAGAAAGAGTCCACCCTGCACCTGATGCTATGCCTGCGAGGTGGCATCATGGAGCCT
TCCCTCTGCCAGCTGGTCCAGAAATACAACTTCGACAAGAGGAAGTGATGTGCTCGCCTACGCCCCCGTGCTGTCAACTG
CCGCAAGTACAACCACACCAACAACCTGTACCCCAAAAAG

Alignment

ORF - retro_cjac_2002 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.8 %
• Parental protein coverage: 97.66 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLV
          M.IFVKTLTGKT..LEVEP.DT..NVKA.I.D..GI.PDQQ.LIF..KQLEDG.TL.D.NIQKESTLHL.
Retrocopy MWIFVKTLTGKTTALEVEPRDTTANVKANIRDN*GILPDQQCLIFESKQLEDGHTLLDCNIQKESTLHLM

Parental  LRLRGGIIEPSLRQLAQKYNCDKMICRKCYARLHPRAVNCRKKKCGHTNNLRPKK
          L.LRGGI.EPSL.QL.QKYN.DK...RK..ARL.PRAVNCR..K..HTNNL.PKK
Retrocopy LCLRGGIMEPSLCQLVQKYNFDK---RK*CARLRPRAVNCR--KYNHTNNLYPKK

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	0.40 RPM	85.95 RPM
SRP051959_heart	0.39 RPM	106.63 RPM
SRP051959_kidney	0.51 RPM	117.88 RPM
SRP051959_liver	0.52 RPM	121.58 RPM
SRP051959_lung	0.39 RPM	156.83 RPM
SRP051959_lymph_node	0.57 RPM	216.41 RPM
SRP051959_skeletal_muscle	0.28 RPM	136.42 RPM
SRP051959_spleen	0.29 RPM	165.59 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2002 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2002 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2002 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1142
Gorilla gorilla	retro_ggor_1265
Macaca mulatta	retro_mmul_1580

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 110 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011356	10 retrocopies	retro_amel_1045, retro_amel_1416, retro_amel_1455, retro_amel_1759, retro_amel_1849, retro_amel_214, retro_amel_800, retro_amel_904, retro_amel_941, retro_amel_973,
Bos taurus	ENSBTAG00000007737	3 retrocopies	retro_btau_1059, retro_btau_1318, retro_btau_832,
Callithrix jacchus	ENSCJAG00000007470	22 retrocopies	retro_cjac_1363, retro_cjac_1388, retro_cjac_1426, retro_cjac_1485, retro_cjac_1521, retro_cjac_1561, retro_cjac_1731, retro_cjac_1743, retro_cjac_2002 , retro_cjac_207, retro_cjac_2254, retro_cjac_2292, retro_cjac_2413, retro_cjac_2501, retro_cjac_2505, retro_cjac_2898, retro_cjac_3054, retro_cjac_658, retro_cjac_683, retro_cjac_883, retro_cjac_892, retro_cjac_898,
Equus caballus	ENSECAG00000020660	8 retrocopies	retro_ecab_1014, retro_ecab_107, retro_ecab_313, retro_ecab_641, retro_ecab_772, retro_ecab_835, retro_ecab_836, retro_ecab_857,
Felis catus	ENSFCAG00000009745	14 retrocopies	retro_fcat_1159, retro_fcat_1204, retro_fcat_1226, retro_fcat_1232, retro_fcat_1382, retro_fcat_1428, retro_fcat_1449, retro_fcat_1540, retro_fcat_1661, retro_fcat_86, retro_fcat_876, retro_fcat_909, retro_fcat_939, retro_fcat_989,
Homo sapiens	ENSG00000221983	2 retrocopies	retro_hsap_2622, retro_hsap_4004,
Latimeria chalumnae	ENSLACG00000008132	1 retrocopy	retro_lcha_11,
Mustela putorius furo	ENSMPUG00000015527	8 retrocopies	retro_mputfur_1059, retro_mputfur_1119, retro_mputfur_1126, retro_mputfur_382, retro_mputfur_516, retro_mputfur_713, retro_mputfur_78, retro_mputfur_945,
Mus musculus	ENSMUSG00000090137	3 retrocopies	retro_mmus_101, retro_mmus_129, retro_mmus_31,
Ochotona princeps	ENSOPRG00000004784	6 retrocopies	retro_opri_1016, retro_opri_144, retro_opri_219, retro_opri_458, retro_opri_644, retro_opri_787,
Pongo abelii	ENSPPYG00000009746	2 retrocopies	retro_pabe_111, retro_pabe_3291,
Pan troglodytes	ENSPTRG00000039223	8 retrocopies	retro_ptro_1142, retro_ptro_1767, retro_ptro_2607, retro_ptro_2718, retro_ptro_2815, retro_ptro_792, retro_ptro_895, retro_ptro_919,
Rattus norvegicus	ENSRNOG00000019974	7 retrocopies	retro_rnor_1125, retro_rnor_1458, retro_rnor_2115, retro_rnor_2472, retro_rnor_2487, retro_rnor_2901, retro_rnor_944,
Sorex araneus	ENSSARG00000000984	11 retrocopies	retro_sara_145, retro_sara_164, retro_sara_192, retro_sara_256, retro_sara_281, retro_sara_331, retro_sara_344, retro_sara_599, retro_sara_67, retro_sara_687, retro_sara_94,
Sarcophilus harrisii	ENSSHAG00000007075	3 retrocopies	retro_shar_405, retro_shar_434, retro_shar_703,
Ictidomys tridecemlineatus	ENSSTOG00000004678	1 retrocopy	retro_itri_49,
Xiphophorus maculatus	ENSXMAG00000003911	1 retrocopy	retro_xmac_6,