RetrogeneDB ID: retro_cjac_2356

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:99389263..99389856(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000032808
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PRDX2
• Ensembl ID: ENSCJAG00000004882
• Aliases: None
• Description: peroxiredoxin 2 [Source:HGNC Symbol;Acc:9353]

Sequence

>retro_cjac_2356
ATGGCCTCTGTAATCGTAGGCATGGGAAAGCCCGCCCCTGACTACAAGGCCACTGCCATAGTGGATGGTGCTTTCAGAGA
GGTGAAGCTGTTGGACTACAAAGAGAGGTACATGGCCCTCTTTTTCTACCCTCTGGACTTCACTTTTGTGTGCCCCATGG
AGATCATCTTGTTCAGTGACCATGCCAAGAACTTCTGCAAGCTGGGCTGTGAAGTGCTGGGCATTTCTGTGGACTCTCAG
TTCACCCACCTGGCTTGGATCAACAACCTCCAGAAGGAGGGAGGCTTGGCCCTCCAAACATCCCCCTGCTTGTTGATGTG
ACCAAAAGCTTATCTGAGAATTATGACATGCTGAAAACAGACGCAGACATTGCCTACAGAGGCTGCTTTATCAATGATGG
CAAGTGGGTCCTTCCCCAGATCACTGTTCATGAGTTGCCTGTGGGATGCTCCATGGATGAGGCTCTGCTGCTGGTCCAGG
CCTTCCAGTACATGAAAGAGCACAGGGAAGTTGGTCCTGCTGGCTGGAAGCCTGGCAGTGACACAATTAAGCCCAATGTG
GATGACAGCAAGGAATATTTCTCCAAACACAAT

Alignment

ORF - retro_cjac_2356 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.88 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MASGNAHIGKPAPDFKATAVVDGAFKEVKLSDYKGKYVVLFFYPLDFTFVCPTEIIAFSNRAEDFRKLGC
          MAS.....GKPAPD.KATA.VDGAF.EVKL.DYK..Y..LFFYPLDFTFVCP.EII.FS..A..F.KLGC
Retrocopy MASVIVGMGKPAPDYKATAIVDGAFREVKLLDYKERYMALFFYPLDFTFVCPMEIILFSDHAKNFCKLGC

Parental  EVLGVSVDSQFTHLAWINTPRKEGGL-GPLNIPLLADVTRRLSEDYGVLKTDEGIAYRGLFVIDGKGVLR
          EVLG.SVDSQFTHLAWIN...KEGGL.GP.NIPLL.DVT..LSE.Y..LKTD..IAYRG.F..DGK.VL.
Retrocopy EVLGISVDSQFTHLAWINNLQKEGGL<GPPNIPLLVDVTKSLSENYDMLKTDADIAYRGCFINDGKWVLP

Parental  QITVNDLPVGRSVDEALRLVQAFQYTDEHGEVCPAGWKPGSDTIKPNVDDSKEYFSKHN
          QITV..LPVG.S.DEAL.LVQAFQY..EH.EV.PAGWKPGSDTIKPNVDDSKEYFSKHN
Retrocopy QITVHELPVGCSMDEALLLVQAFQYMKEHREVGPAGWKPGSDTIKPNVDDSKEYFSKHN

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	21.26 RPM
SRP051959_heart	0.00 RPM	36.59 RPM
SRP051959_kidney	0.00 RPM	32.39 RPM
SRP051959_liver	0.00 RPM	13.56 RPM
SRP051959_lung	0.00 RPM	11.16 RPM
SRP051959_lymph_node	0.00 RPM	1.85 RPM
SRP051959_skeletal_muscle	0.00 RPM	40.99 RPM
SRP051959_spleen	0.00 RPM	12.40 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2356 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2356 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2356 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_1780

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Parental genes homology:

Parental genes homology involve 23 parental genes, and 48 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012307	3 retrocopies	retro_amel_1188, retro_amel_1710, retro_amel_55,
Canis familiaris	ENSCAFG00000017163	3 retrocopies	retro_cfam_1603, retro_cfam_1624, retro_cfam_1739,
Ciona intestinalis	ENSCING00000003002	1 retrocopy	retro_cint_8,
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,
Dipodomys ordii	ENSDORG00000009005	1 retrocopy	retro_dord_176,
Felis catus	ENSFCAG00000000473	1 retrocopy	retro_fcat_1755,
Homo sapiens	ENSG00000167815	3 retrocopies	retro_hsap_1184, retro_hsap_3278, retro_hsap_3500,
Gorilla gorilla	ENSGGOG00000025089	3 retrocopies	retro_ggor_2366, retro_ggor_2833, retro_ggor_923,
Macaca mulatta	ENSMMUG00000005689	2 retrocopies	retro_mmul_1780, retro_mmul_2061,
Monodelphis domestica	ENSMODG00000006978	1 retrocopy	retro_mdom_1770,
Mustela putorius furo	ENSMPUG00000004591	2 retrocopies	retro_mputfur_28, retro_mputfur_660,
Mus musculus	ENSMUSG00000005161	2 retrocopies	retro_mmus_2403, retro_mmus_472,
Nomascus leucogenys	ENSNLEG00000012800	2 retrocopies	retro_nleu_2110, retro_nleu_2883,
Otolemur garnettii	ENSOGAG00000024998	2 retrocopies	retro_ogar_1993, retro_ogar_244,
Pongo abelii	ENSPPYG00000009607	3 retrocopies	retro_pabe_2711, retro_pabe_2892, retro_pabe_988,
Pan troglodytes	ENSPTRG00000010541	3 retrocopies	retro_ptro_2217, retro_ptro_2372, retro_ptro_812,
Rattus norvegicus	ENSRNOG00000003520	2 retrocopies	retro_rnor_2288, retro_rnor_497,
Sorex araneus	ENSSARG00000000146	1 retrocopy	retro_sara_96,
Sarcophilus harrisii	ENSSHAG00000015596	1 retrocopy	retro_shar_305,
Sus scrofa	ENSSSCG00000013736	2 retrocopies	retro_sscr_155, retro_sscr_962,
Ictidomys tridecemlineatus	ENSSTOG00000025862	1 retrocopy	retro_itri_842,