RetrogeneDB ID: retro_cjac_499

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:201173..202464(-)
• 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_499
AGTGAGCCCTTCTTCAAGGCCAACGCAGAGGAGGAGCTCAAGCCGGAGGACTTCTTTACCCGCAACTCCTATGTGGCCGG
CCAGTAAAATGATGCAGCCTCCGACTAGCACCTCAACAGCCACATGAATGCCTTCCACCGGGGATCACAGGCCAACCATC
TCTTCTACCTGGCCTTGCCTTCCACGGTCTGTGAGGCCGTCACCAAGAACATCCACAAGTCCTGCATGAGCCAGACAGGC
TGGAACCGCATCATCGTGGAGAAGCCCTTCGGGAGGGAGCTGTGGAGCTCCAAGCGGCTGTCCAACCATATCTCCTCCCT
GTTCCGTGAGGACCAGATCTAGCGCATCGACCACTACCTGGGCAAGGAGATGGTGCAAAGCCTCATGGTGCTGATATTTG
CCAACAGGATCTTCAACTCCATCTGGAACCGGGACCACATCACCTGCGTGATCCTCACCTTCAAGGAGCCCTATGGCACT
GAGGGTCACGGAGGCTATTTCGATGAATTTGGGATCACCTGGGACATGATGCAGAGCCACCTCCTGCAGATGCTGTGTCT
GGTGGCCATGGAGAAGCCCACCTCCACCAACTCGGATGATGTCCGTGATGAGCAGGTCAAGGTGTTGAAATGCATCTCAG
GGGTACAGGCAAACAACGTAGTCCTGGGCCAGTACGTGAGGAACCCCGAGGGAGAGGGCAAGGCCACCAAAGGATACCAG
ATGCCCCCCTGGTGCCTCACGGGTCCACCACCGCCACCTTTGCCGTCGTCCTCTACGTGGAGAACTAGAGGTGGGATGGG
GTGCCGTTCATCCTGCGCTGCCGCAAGGCCATTAACGAGCGCAAGGCCGAGGTGAGGCTGCAGTTCCGCAAGGTGGCTGG
TGACATCTTCCACCAGCAGTGCAGGCGCAATGAGCTGGTGATCCACATGCAGCCCCACGAGGCCATATACATCAAGATGA
TGACCAAGAAGCCGAGCATGTTCTTCATCCCTGAGGAGTAGGAGCTGGACCTGAACTACCGCAACAGATAGAAGAACTGG
AAGCTCCCTGGCACCTAGGAGCGCCTCCTCCTGGACATCTTCTGCAGGAGCCAGATGTACTTCCTGCCCAGCGACGAGCT
CCAGGAGGCCTGGCAGATCTTTACCCCGTTGCTGCACCAGATGGAGCAGCAGAAGCCCCAGCCCATCCCCTACGTCTATG
GCAGCCGAGTTCCACAGAGACAGACGAGCTGATGAAGAGAGTGGGTTTCAAGCATGAGGGTACCTTCAAGTGGGTGAACC
CCCACAAGCTC

Alignment

ORF - retro_cjac_499 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.03 %
• Parental protein coverage: 83.88 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SEPFFKTTPKEKLKLEDFFACNSYVAGQYDDAASYQRLSSHMNALHQGSQANRLFYLALPPTVYEAVTKN
          SEPFFK....E.LK.EDFF..NSYVAGQ..DAAS...L.SHMNA.H.GSQAN.LFYLALP.TV.EAVTKN
Retrocopy SEPFFKANAEEELKPEDFFTRNSYVAGQ*NDAASD*HLNSHMNAFHRGSQANHLFYLALPSTVCEAVTKN

Parental  IHEFCMSQTGWNRIIVEKPFGRDLQSSDRLSNHISSLFREDQIYRIDHYLGKEMVQNLMVLRFANRIFGP
          IH..CMSQTGWNRIIVEKPFGR.L.SS.RLSNHISSLFREDQI.RIDHYLGKEMVQ.LMVL.FANRIF..
Retrocopy IHKSCMSQTGWNRIIVEKPFGRELWSSKRLSNHISSLFREDQI*RIDHYLGKEMVQSLMVLIFANRIFNS

Parental  IWNRDNIACVILTFKEPFGTEGRGGYFDEFGIIRDVMQNHLLQMLCLVAMEKPASTNSDDVRDEKVKVLK
          IWNRD.I.CVILTFKEP.GTEG.GGYFDEFGI..D.MQ.HLLQMLCLVAMEKP.STNSDDVRDE.VKVLK
Retrocopy IWNRDHITCVILTFKEPYGTEGHGGYFDEFGITWDMMQSHLLQMLCLVAMEKPTSTNSDDVRDEQVKVLK

Parental  CISEVQASNVVLGQYVGNPDGEGEAAKGYL-DDPTVPRGSTTATFAAVVLYVENERWDGVPFILRCGKAL
          CIS.VQA.NVVLGQYV.NP.GEG.A.KGY..D.P.VP.GSTTATF.AVVLYVEN.RWDGVPFILRC.KA.
Retrocopy CISGVQANNVVLGQYVRNPEGEGKATKGYQ<DAPLVPHGSTTATF-AVVLYVEN*RWDGVPFILRCRKAI

Parental  NERKAEVRLQFHDVAGDIFHQQCKRNELVIRVQPNEAVYTKMMTKKPGMFFNPEESELDLTYGNRYKNVK
          NERKAEVRLQF..VAGDIFHQQC.RNELVI..QP.EA.Y.KMMTKKP.MFF.PEE.ELDL.Y.NR.KN.K
Retrocopy NERKAEVRLQFRKVAGDIFHQQCRRNELVIHMQPHEAIYIKMMTKKPSMFFIPEE*ELDLNYRNR*KNWK

Parental  LPDAYERLILDVFCGSQMHFVRSDELREAWRIFTPLLHQIELEKPQPIPYLYGSRGP-TEADELMKKVGF
          LP...ERL.LD.FC.SQM.F..SDEL.EAW.IFTPLLHQ.E..KPQPIPY.YGSR.P.TE.DELMK.VGF
Retrocopy LPGT*ERLLLDIFCRSQMYFLPSDELQEAWQIFTPLLHQMEQQKPQPIPYVYGSRVP<TETDELMKRVGF

Parental  QYEGTYKWVNPHKL
          ..EGT.KWVNPHKL
Retrocopy KHEGTFKWVNPHKL

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	0.02 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_499 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_499 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_499 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,