RetrogeneDB ID: retro_cjac_4066

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:53494061..53494994(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000007345
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FOXR1
• Ensembl ID: ENSCJAG00000013656
• Aliases: None
• Description: forkhead box R1 [Source:HGNC Symbol;Acc:29980]

Sequence

>retro_cjac_4066
ATGGACTTAAAACTAAAAGATCTTGAATTTTGGTATAATCTCCAAGGCCAGGTACCAGGGCTGCTGGACTGGGACATGCA
GAATGAGTTATTTTTGTCTTGTACCACAGACCAGTGCTCCTTAACTGAGCAGCTCCTTAGCAAATATAGAATTCGAGTAA
TGAAGCCCCCAGAGATGCCTCAGAATAGGACACTCAGTCCTAATAAAGATGGTCCTCACTGTGAACCCAATCTGTGGATA
TGGGTGAACCCCAACATTCTGTGCCCCCTTGGCAGCCAGAAGGCCCCAAAGCCCATTGGAAAAAAGGATACGACAAGCAT
TTCTCCTTTCCCTCAGCCCTCACTAACAGATGAAGAGTCCAGCTGCTCAGAGGTCACAGTGGTAGAGTCCCTGTCATCTT
CCTCCAGTGAGCAGTCTCCTATACAGAAGCAAGATATCTATTCCCCTAACAACTTCGTGCTCACAGAAGAGGAGGCTGAG
AAACAAGAGGACAACTCCTTCCAGTCCTCTGAAAGGGAGTGCTTCCAGAGCCAGAAGCTATGGCAAATCAACAAGCAAGA
GAAGTCCTGGCAACGGATCCCTCTCAATTGTAGCCACCTTATTGCCCTAGCATTAAGAAAGAGCCCCCACTATGGCCTCA
GTGTGAAGGAGATCTACAGTTTCACCCAACACCATTTCCCCTTTTTCCGGACAGCTCCAGATGGCTGGAAGAGCACCATT
CATTATAACCTCTGCTTCCTGAGCAGCTTTGAGAAGGTACCAGACGACCTTCAGGGTGAAAATAATGCAAGATCTTGCTG
TTGCCGTTGGAGGCTCACTAAAGAGGGGCACCGCCGCTTTTTGGAGGAAACTCGTGCCTTAGCTGCTGCTCAAAGGGAGA
GCATCCAAGAGTGCATGAGTCAGCCAGACCTGTTTACCTCTCTCTTTGATCTT

Alignment

ORF - retro_cjac_4066 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.77 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VDVKLQHLDFWASLHGQVPGLLDWDMGNELFLAFTTSHLPLAEQKLARYKLRIVKPPKLPLEKKTNPDKD
          .D.KL..L.FW..L.GQVPGLLDWDM.NELFL..TT....L.EQ.L..Y..R..KPP..P......P.KD
Retrocopy MDLKLKDLEFWYNLQGQVPGLLDWDMQNELFLSCTTDQCSLTEQLLSKYRIRVMKPPEMPQNRTLSPNKD

Parental  GPDYEPNLWMWVNPNIVYPPGKLEVPGLMKKEDLTSTLPSSQPFQKEEDASCSEPTGAESLSRSSSEWSP
          GP..EPNLW.WVNPNI..P.G....P....K.D.TS..P..QP....E..SCSE.T..ESLS.SSSE.SP
Retrocopy GPHCEPNLWIWVNPNILCPLGSQKAPKPIGKKDTTSISPFPQPSLTDEESSCSEVTVVESLSSSSSEQSP

Parental  PQKRFAFSPSIWELTEEEEAEDQEDSSSVALPSPHKKAPLQSRRLRQASSQAGRLWSRPPLNYFHLIALA
          .QK....SP....LTE....E..E........S.......QS..L.Q...Q....W.R.PLN..HLIALA
Retrocopy IQKQDIYSPNNFVLTE----EEAEKQEDNSFQSSEREC-FQSQKLWQINKQE-KSWQRIPLNCSHLIALA

Parental  LRNSSPCGLNVQQIYSFTRKHFPFFRTAPEGWKNTVRHNLCFRDSFEKVPVSSVQGGASARPRSCLWKLT
          LR.S...GL.V..IYSFT..HFPFFRTAP.GWK.T...NLCF..SFEKVP....QG...AR...C.W.LT
Retrocopy LRKSPHYGLSVKEIYSFTQHHFPFFRTAPDGWKSTIHYNLCFLSSFEKVP-DDLQGENNARSCCCRWRLT

Parental  EEGHRRFEEEARALASTRLESIQRCMSQPDVMPFLFDL
          .EGHRRF.EE.RALA....ESIQ.CMSQPD....LFDL
Retrocopy KEGHRRFLEETRALAAAQRESIQECMSQPDLFTSLFDL

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	0.11 RPM
SRP051959_heart	0.02 RPM	0.14 RPM
SRP051959_kidney	0.00 RPM	0.07 RPM
SRP051959_liver	0.00 RPM	0.17 RPM
SRP051959_lung	0.02 RPM	0.28 RPM
SRP051959_lymph_node	0.00 RPM	0.39 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.02 RPM
SRP051959_spleen	0.02 RPM	0.25 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4066 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4066 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4066 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_72
Pan troglodytes	retro_ptro_94
Pongo abelii	retro_pabe_69
Bos taurus	retro_btau_189

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000053	1 retrocopy	retro_amel_39,
Bos taurus	ENSBTAG00000014606	1 retrocopy	retro_btau_189,
Canis familiaris	ENSCAFG00000012417	1 retrocopy	retro_cfam_209,
Callithrix jacchus	ENSCJAG00000013656	1 retrocopy	retro_cjac_4066 ,
Dasypus novemcinctus	ENSDNOG00000009414	1 retrocopy	retro_dnov_22,
Dipodomys ordii	ENSDORG00000001960	1 retrocopy	retro_dord_651,
Homo sapiens	ENSG00000176302	1 retrocopy	retro_hsap_72,
Microcebus murinus	ENSMICG00000002680	1 retrocopy	retro_mmur_38,
Macaca mulatta	ENSMMUG00000022722	1 retrocopy	retro_mmul_125,
Mustela putorius furo	ENSMPUG00000004890	1 retrocopy	retro_mputfur_161,
Nomascus leucogenys	ENSNLEG00000007376	1 retrocopy	retro_nleu_50,
Otolemur garnettii	ENSOGAG00000007258	1 retrocopy	retro_ogar_296,
Procavia capensis	ENSPCAG00000010132	1 retrocopy	retro_pcap_12,
Pongo abelii	ENSPPYG00000003947	1 retrocopy	retro_pabe_69,
Pan troglodytes	ENSPTRG00000004358	1 retrocopy	retro_ptro_94,
Sorex araneus	ENSSARG00000011319	1 retrocopy	retro_sara_38,
Sus scrofa	ENSSSCG00000015101	1 retrocopy	retro_sscr_36,
Ictidomys tridecemlineatus	ENSSTOG00000014321	1 retrocopy	retro_itri_158,