RetrogeneDB ID: retro_cjac_4026

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL289587.1:4632..5931(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: G6PD
• Ensembl ID: ENSCJAG00000016775
• Aliases: None
• Description: Glucose-6-phosphate 1-dehydrogenase [Source:UniProtKB/TrEMBL;Acc:B0KWT9]

Sequence

>retro_cjac_4026
ATGGCCGAGCAGGTGGCCCTGAGCCGGACCCAGGTGTGAGGGATCCTCTGGGAAGAGCTGCTCTGGGGACAATGCCTTCC
ATCAGTCGGATACACACATAGTCATCATGATGGGTGCATCAGGTGAGCTGGCCAGGAGGAAGATCTACCCCTCCATCTGG
TGGCTGTTCCGGGATGGCCTTCTGCCGGAAAATACCTTCCTCATGGGCTACGCCCGCTCCCGCCTCACAGTGGCTGACAT
CCGCAAGCAAAGTGAGCCCTTCTTCAAGGCCAACGCAGAGGAGGAGCTCAAGCCGGAGGACTTCTTTACCCGCAACTCCT
ATGTGGCCGGCCAGTAAAATGATGCAGCCTCCGACTAGCACCTCAACAGCCACATGAACGCCTTCCACCGGGGATCACAG
GCCAACCAGCTCTTCTACCTGGCCTTGCCTTCCACGGTCTATGAGGCCATCACCAAGAACATCCACAAGTCCTGCATGAG
CCAGACAGGCTGGAACTGCATCATCGTGGAGAAGCCCTTCGGGAGGGAGCTGCGGAGCTCCGAGCGGCTGTCCAACCATA
TCTCCTCCCTGTTCCGCGAGGACCAGATCTATCGCATCGACCACTACCTGGTCAAGGAAATGGTGCAAAGCCTCATGGTG
CTGAGATTTGCCAACAGGATCTTCAACTCCATCTGGAACTGAGACCACATCACCTGCGTGATCCTCACCTTCAAGGAGCC
CTATGGCACTGAGGGTCACGGAGGCTATTTCGATGAATTTGGGATCACCTGGGACATGATGCAGAGCCACCTCCTGCAGA
TGCTGTGTCTTGTGGCCATGGAGAAGCCCACCTCCACCAACTCGGATGATGTCCGTGATGAGCAGGTCAAGGTGTTGAAA
TGCATCTCAGGGGTACAGGCAAACAACGTAGTCCTGGGCCAGTACGTGAGGAACCCCGAGGGAGAGGGCAAGGCCACCAA
AGGATACCAGATGCCCCCCTGGTGCCTCACGGGTCCACCACCACCACCTTTGCCATCATCCTCTACCTGGAAAACTAGAG
GTGGGATGGGGTGCCCTTCATCCTGCGCTATCGCAAGGCCGTTAATGAGCACAAGGCCGAGGTGAGGCTGCAGTTCCGCA
AGGTGGCTGGTGACATCTTCCACCAGCAGTGCAGGCGCAATGAGCTGGTGATCCGCATGCGGCCCCACGAGGCCATATAC
ATCAAGATGATGACCAAGAAGCCGAGCATGTTCTTCATCCCCGAGGAGTAGGAGCTGGACCTGACCTATGGCAACAGATG
GAAGAACTGGAAGCTCCCT

Alignment

ORF - retro_cjac_4026 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.82 %
• Parental protein coverage: 84.27 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAEQVALSRTQVCGILREELFQG-DAFHQSDTHIFIIMGASGDLAKKKIYPTIWWLFRDGLLPENTFIVG
          MAEQVALSRTQV.GIL.EEL..G..AFHQSDTHI.I.MGASG.LA..KIYP.IWWLFRDGLLPENTF..G
Retrocopy MAEQVALSRTQV*GILWEELLWG>NAFHQSDTHIVIMMGASGELARRKIYPSIWWLFRDGLLPENTFLMG

Parental  YARSRLTVADIRKQSEPFFKTTPKEKLKLEDFFACNSYVAGQYDDAASYQRLSSHMNALHQGSQANRLFY
          YARSRLTVADIRKQSEPFFK....E.LK.EDFF..NSYVAGQ..DAAS...L.SHMNA.H.GSQAN.LFY
Retrocopy YARSRLTVADIRKQSEPFFKANAEEELKPEDFFTRNSYVAGQ*NDAASD*HLNSHMNAFHRGSQANQLFY

Parental  LALPPTVYEAVTKNIHEFCMSQTGWNRIIVEKPFGRDLQSSDRLSNHISSLFREDQIYRIDHYLGKEMVQ
          LALP.TVYEA.TKNIH..CMSQTGWN.IIVEKPFGR.L.SS.RLSNHISSLFREDQIYRIDHYL.KEMVQ
Retrocopy LALPSTVYEAITKNIHKSCMSQTGWNCIIVEKPFGRELRSSERLSNHISSLFREDQIYRIDHYLVKEMVQ

Parental  NLMVLRFANRIFGPIWNRDNIACVILTFKEPFGTEGRGGYFDEFGIIRDVMQNHLLQMLCLVAMEKPAST
          .LMVLRFANRIF..IWN.D.I.CVILTFKEP.GTEG.GGYFDEFGI..D.MQ.HLLQMLCLVAMEKP.ST
Retrocopy SLMVLRFANRIFNSIWN*DHITCVILTFKEPYGTEGHGGYFDEFGITWDMMQSHLLQMLCLVAMEKPTST

Parental  NSDDVRDEKVKVLKCISEVQASNVVLGQYVGNPDGEGEAAKGYL-DDPTVPRGSTTATFAAVVLYVENER
          NSDDVRDE.VKVLKCIS.VQA.NVVLGQYV.NP.GEG.A.KGY..D.P.VP.GSTT.TF.A..LY.EN.R
Retrocopy NSDDVRDEQVKVLKCISGVQANNVVLGQYVRNPEGEGKATKGYQ<DAPLVPHGSTTTTF-AIILYLEN*R

Parental  WDGVPFILRCGKALNERKAEVRLQFHDVAGDIFHQQCKRNELVIRVQPNEAVYTKMMTKKPGMFFNPEES
          WDGVPFILR..KA.NE.KAEVRLQF..VAGDIFHQQC.RNELVIR..P.EA.Y.KMMTKKP.MFF.PEE.
Retrocopy WDGVPFILRYRKAVNEHKAEVRLQFRKVAGDIFHQQCRRNELVIRMRPHEAIYIKMMTKKPSMFFIPEE*

Parental  ELDLTYGNRYKNVKLP
          ELDLTYGNR.KN.KLP
Retrocopy ELDLTYGNRWKNWKLP

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	11.71 RPM
SRP051959_heart	0.00 RPM	5.96 RPM
SRP051959_kidney	0.00 RPM	11.16 RPM
SRP051959_liver	0.00 RPM	4.03 RPM
SRP051959_lung	0.00 RPM	9.99 RPM
SRP051959_lymph_node	0.00 RPM	8.45 RPM
SRP051959_skeletal_muscle	0.00 RPM	2.51 RPM
SRP051959_spleen	0.00 RPM	21.34 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4026 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4026 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4026 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016775	2 retrocopies	retro_cjac_4026 , retro_cjac_499,
Equus caballus	ENSECAG00000014994	1 retrocopy	retro_ecab_492,
Myotis lucifugus	ENSMLUG00000008210	1 retrocopy	retro_mluc_842,
Mus musculus	ENSMUSG00000031400	1 retrocopy	retro_mmus_174,
Sus scrofa	ENSSSCG00000025108	1 retrocopy	retro_sscr_818,