RetrogeneDB ID: retro_cjac_3082

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 8:73644618..73645227(+)
• Located in intron of: ENSCJAG00000016056

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRDX3
• Ensembl ID: ENSCJAG00000019636
• Aliases: None
• Description: peroxiredoxin 3 [Source:HGNC Symbol;Acc:9354]

Sequence

>retro_cjac_3082
ATGGCGGCTGATATGGAAAGGTTGCTCTGAGGGTCAGTTGCTTGACATGTGAGTGCCAAACCTTGGGGCATTTCTGCCAC
TGCAACCAACAGGCCTGCTGCAACTGGAAGAATGAGCTTGACAAACATATTGTGGTCTGGTTCTGATCAAGCAAAATTAT
TTACCACCAGTTCCTTATACACATTCACCCGCTGTCATCTGGCATGCACCTTATTTTAAGGGTACAGCCATTGTCAATGG
AGAGATGGAGAGTTCAAAGACCTAAAGCTTGATGACTTTAAAAGGGAAATTTTTGGTGCTTTTCTTCTATCCTTTGGATT
TCACCTTGGGTATCCTACAGAAACTGTTGCTTTTAGTGACAAAGATAAGGAGTTTGCCAATGTGAACTGTGAAGTTGTTT
CGGTCTCAGTGGATTCCCACTTTAGTCATCTTGCCTAGATAAATACACCAAGAAAGAATGGCAGTTTGGGGTACATGAAC
ATTGCACTCTTGTCAGATTTAACTAGGCAAATTTCCCAAGACAATGGTGTGCTGTTAGAAGGTCCTGGTTTTGCACTAAG
AGGTCTCTTCATAATCAACCCCAACGGAGTCACCAAGCACTTAAGTGTC

Alignment

ORF - retro_cjac_3082 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.66 %
• Parental protein coverage: 78.12 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAAAVRRLLRSSVARHVSSLPWGISATAALRPAVCGRTSLTNILCSGSGQAKFFSSSSSY-HAPAVTQHA
          MAA...RLL..SVA.HVS..PWGISATA..RPA..GR.SLTNIL.SGS.QAK.F..SS.Y.H.PAV..HA
Retrocopy MAADMERLL*GSVA*HVSAKPWGISATATNRPAATGRMSLTNILWSGSDQAKLFTTSSLY>HSPAVIWHA

Parental  PYFKGTAVVNGEF---KDLSLDDFKGKYLVLFFYPLDFTFVC-PTEIIAFSDKVNEFHDVNCEVVAVSVD
          PYFKGTA.VNGE....K..SL...KGK.LVLFFYPLDFT....PTE..AFSDK..EF..VNCEVV.VSVD
Retrocopy PYFKGTAIVNGEMESSKT*SLMTLKGKFLVLFFYPLDFTLGI<PTETVAFSDKDKEFANVNCEVVSVSVD

Parental  SHFSHLAWINTPRKNGGLGHMNIALLSDLTKQISRDYGVLLEGPGLALRGLFIIDPNGVIKHLSV
          SHFSHLA.INTPRKNG.LG.MNIALLSDLT.QIS.D.GVLLEGPG.ALRGLFII.PNGV.KHLSV
Retrocopy SHFSHLA*INTPRKNGSLGYMNIALLSDLTRQISQDNGVLLEGPGFALRGLFIINPNGVTKHLSV

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	0.31 RPM	36.85 RPM
SRP051959_heart	0.23 RPM	55.83 RPM
SRP051959_kidney	0.60 RPM	83.46 RPM
SRP051959_liver	0.26 RPM	121.08 RPM
SRP051959_lung	0.65 RPM	23.59 RPM
SRP051959_lymph_node	0.59 RPM	25.59 RPM
SRP051959_skeletal_muscle	0.26 RPM	74.97 RPM
SRP051959_spleen	0.48 RPM	34.54 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3082 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3082 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3082 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 50 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000008731	1 retrocopy	retro_btau_562,
Canis familiaris	ENSCAFG00000012109	3 retrocopies	retro_cfam_1322, retro_cfam_219, retro_cfam_9,
Callithrix jacchus	ENSCJAG00000004807	2 retrocopies	retro_cjac_1201, retro_cjac_2884,
Callithrix jacchus	ENSCJAG00000004882	4 retrocopies	retro_cjac_1269, retro_cjac_1795, retro_cjac_2356, retro_cjac_2392,
Callithrix jacchus	ENSCJAG00000019636	3 retrocopies	retro_cjac_1333, retro_cjac_3082 , retro_cjac_653,
Ciona savignyi	ENSCSAVG00000001209	1 retrocopy	retro_csav_6,
Dasypus novemcinctus	ENSDNOG00000001359	3 retrocopies	retro_dnov_1052, retro_dnov_2373, retro_dnov_745,
Equus caballus	ENSECAG00000017026	1 retrocopy	retro_ecab_408,
Erinaceus europaeus	ENSEEUG00000009299	1 retrocopy	retro_eeur_238,
Homo sapiens	ENSG00000165672	3 retrocopies	retro_hsap_1253, retro_hsap_2587, retro_hsap_2653,
Gorilla gorilla	ENSGGOG00000026364	1 retrocopy	retro_ggor_986,
Macropus eugenii	ENSMEUG00000007732	3 retrocopies	retro_meug_1219, retro_meug_1735, retro_meug_62,
Microcebus murinus	ENSMICG00000007627	1 retrocopy	retro_mmur_475,
Myotis lucifugus	ENSMLUG00000012871	3 retrocopies	retro_mluc_1203, retro_mluc_1522, retro_mluc_2069,
Macaca mulatta	ENSMMUG00000008294	2 retrocopies	retro_mmul_1307, retro_mmul_1517,
Monodelphis domestica	ENSMODG00000009286	1 retrocopy	retro_mdom_1062,
Mustela putorius furo	ENSMPUG00000003074	1 retrocopy	retro_mputfur_1032,
Nomascus leucogenys	ENSNLEG00000016698	3 retrocopies	retro_nleu_1521, retro_nleu_2118, retro_nleu_2453,
Oryctolagus cuniculus	ENSOCUG00000017334	2 retrocopies	retro_ocun_135, retro_ocun_1434,
Pongo abelii	ENSPPYG00000002700	1 retrocopy	retro_pabe_1906,
Pan troglodytes	ENSPTRG00000002992	1 retrocopy	retro_ptro_29,
Ictidomys tridecemlineatus	ENSSTOG00000002537	2 retrocopies	retro_itri_1098, retro_itri_1753,
Tupaia belangeri	ENSTBEG00000011064	5 retrocopies	retro_tbel_3138, retro_tbel_3994, retro_tbel_710, retro_tbel_770, retro_tbel_811,
Tursiops truncatus	ENSTTRG00000010878	2 retrocopies	retro_ttru_1703, retro_ttru_881,