RetrogeneDB ID: retro_cjac_1795

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:59163689..59164226(+)
• Located in intron of: ENSCJAG00000009844

Retrocopy information

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

Parental gene information

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

Sequence

>retro_cjac_1795
ATGGACTCTGGTCAGGCACAGCTCAGAAAGCCAGCCCCTGACTTCAAGGCCACTGCCCTGGTGGATGGCCTTAGGCAGGG
CAAAGCTGTCAACTACAAAGGGAAATACTTCATCCTCTTTTTTTACCCTCTGGACTTCACTTTTCTGTGGCCCACAGAGA
TCATAGTGTTCAGCGACCATGCCGAGGATTTCCATAAGCTGGGTTATGAAGTGCTGGGCATCTCGATGGACTCAGTTCAC
CCACCTGACTTGGATCATCTACAACCCCCGGAAGGAGGGAGGCTTAGGCCCCCTGAGCATCCCCTGCCTATTGACATGAC
AGGAAGCTTGTCCGAGGATTATGGCGTGCTGAAAACAGATGAGGGCATTGCCTAACAGGGCCTCTTTATCATCGATGGCA
GAGGTGACCTTTGCCAGATCACTGTTAATGATTTGCCTGTGGTGTGCTCTGTGGATGAGGCTCTGTGACTGGTCCAGGCC
TTCCAGTACACAGACAAGCACGGGGAAGTTTGTCCCACTGGCTAGAAGCCTGGCAGC

Alignment

ORF - retro_cjac_1795 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.78 %
• Parental protein coverage: 90.82 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MASGNAHIGKPAPDFKATAVVDGAFKEVKLSDYKGKYVVLFFYPLDFTFVCPTEIIAF-ATVPRTSASWE
          M.SG.A...KPAPDFKATA.VDG.....K...YKGKY..LFFYPLDFTF..PTEII.F.AT.PR.S.SW.
Retrocopy MDSGQAQLRKPAPDFKATALVDG-LRQGKAVNYKGKYFILFFYPLDFTFLWPTEIIVF>ATMPRISISWV

Parental  V-LGVSVDSQFTHLAW-INTPRKEGGLGPLNIPLL-ADVTRRLSEDYGVLKTDEGIAYRGLFVIDGKGVL
          .....S...QFTHL.W.I..PRKEGGLGPL.IP.L..D.T..LSEDYGVLKTDEGIA..GLF.IDG.G.L
Retrocopy MKCWASRWTQFTHLTWIIYNPRKEGGLGPLSIPCL<IDMTGSLSEDYGVLKTDEGIA*QGLFIIDGRGDL

Parental  RQITVNDLPVGRSVDEALRLVQAFQYTDEHGEVCPAGWKPGS
          .QITVNDLPV..SVDEAL.LVQAFQYTD.HGEVCP.G.KPGS
Retrocopy CQITVNDLPVVCSVDEAL*LVQAFQYTDKHGEVCPTG*KPGS

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	0.60 RPM	21.26 RPM
SRP051959_heart	0.63 RPM	36.59 RPM
SRP051959_kidney	0.89 RPM	32.39 RPM
SRP051959_liver	0.32 RPM	13.56 RPM
SRP051959_lung	1.56 RPM	11.16 RPM
SRP051959_lymph_node	2.17 RPM	1.85 RPM
SRP051959_skeletal_muscle	0.59 RPM	40.99 RPM
SRP051959_spleen	0.90 RPM	12.40 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1795 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1795 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1795 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3278
Pan troglodytes	retro_ptro_2217
Pongo abelii	retro_pabe_2711

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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,