RetrogeneDB ID: retro_cjac_1333

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 15:40350727..40351282(+)
• Located in intron of: ENSCJAG00000019532

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_1333
TTTAAAGGTACAGCCTTTGTCAATGGAGAGGTCAAAGATCGATGCCTTGATGATTATAAGGGGGAAATATCTGGTTCTTT
TCTTCTATCCTTTGGATTTCACCTTGTGTGTCCAAAACAATTTCTTGCTTTTAATGATAAAGACAATGGACTTTACAAAG
TGAACTGTGAAGTTGTTGCAGACTTAGTGGATTCCCACTTTAGCCATCTTGCCTGGATAAATGTACCAAGAAAGAATGGT
GGTTTGGGACACATGAACATCACACTTTTGTCAGATTTAACTAAACACATTTCCCAAGACTATGGTGTGCCATTAGAAAG
TCGTTGTCTTGCACTAAGAGGAGTCTTCATAATTGACCCCATGAAATTATCAAGCATTTGAGTGTCAATGACTTATCAGT
GGGCTAAAGCATGAAAGAGACCCTCTGCTTGGTGAAGGCATTCCTGTTTGTAAAAAACCCATGGAGAAGTTTGCTCAGCA
AAGTGGACACTGAAGTCTACTACAATCAAGCCAAATCCAACTCTTTCCAAAGAATATTTTGAGAAGGTAAATCAG

Alignment

ORF - retro_cjac_1333 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.02 %
• Parental protein coverage: 72.27 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  FKGTAVVNGEFKDLSLDDFKG-KYLVLFFYPLDFTF-VCPTEIIAFSDKVNEFHDVNCEVVAVSVDSHFS
          FKGTA.VNGE.KD..LDD.KG.KYLVLFFYPLDFT..VCP....AF.DK.N....VNCEVVA..VDSHFS
Retrocopy FKGTAFVNGEVKDRCLDDYKG>KYLVLFFYPLDFTL<VCPKQFLAFNDKDNGLYKVNCEVVADLVDSHFS

Parental  HLAWINTPRKNGGLGHMNIALLSDLTKQISRDYGVLLEGPGLALRGLFIID-PNGVIKHLSVNDLPVGRS
          HLAWIN.PRKNGGLGHMNI.LLSDLTK.IS.DYGV.LE...LALRG.FIID.P...IKHLSVNDL.VG.S
Retrocopy HLAWINVPRKNGGLGHMNITLLSDLTKHISQDYGVPLESRCLALRGVFIID<PHEIIKHLSVNDLSVG*S

Parental  VEETLRLVKAFQYV-ETHGEVCPANWTPDSPTIKPSPDASKEYFQKVNQ
          ..ETL.LVKAF..V..THGEVC.A.WT..S.TIKP.P..SKEYF.KVNQ
Retrocopy MKETLCLVKAFLFV>KTHGEVCSAKWTLKSTTIKPNPTLSKEYFEKVNQ

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	0.42 RPM	36.85 RPM
SRP051959_heart	0.49 RPM	55.83 RPM
SRP051959_kidney	0.07 RPM	83.46 RPM
SRP051959_liver	0.02 RPM	121.08 RPM
SRP051959_lung	1.79 RPM	23.59 RPM
SRP051959_lymph_node	0.37 RPM	25.59 RPM
SRP051959_skeletal_muscle	0.07 RPM	74.97 RPM
SRP051959_spleen	0.19 RPM	34.54 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1333 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1333 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1333 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2653
Macaca mulatta	retro_mmul_1517

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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,