RetrogeneDB ID: retro_cjac_2892

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:69375881..69376981(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PGD
• Ensembl ID: ENSCJAG00000005090
• Aliases: None
• Description: 6-phosphogluconate dehydrogenase, decarboxylating [Source:UniProtKB/TrEMBL;Acc:F7G049]

Sequence

>retro_cjac_2892
CGACACCTCAAGGCCAAGGGAATTTTATTTGTGGGGATCGGAGTCAGTGGAGGAGAGGAAGGGGCTTGGTATGACCCATC
ACTCATGCCAGGAGGGAACAAAGAAGCATGGCCCCACATCAAGACCATCTTCCAAGGCATTGCTGCAAAAGTAGGAACTG
GAGAACCCTGCTGTGACTGGGTGGGAGCAGGCCACTTCATGAAGATGGTGCACAGCAGGATAGAGTATGGGGACATGCAG
CTGATCTGTGAGGCATACCACCTGATGAAAGACGTGCTGGCCATGGTGCAGGACAAGATGGTGCAGGCCTTTGAAGATTG
GAACAAGACAGAGCTAGACTTATTCCTGATTGAAATCACAGCCAATATTCTTAAGTTCCAAGATGCGGATAGCAGACATC
TGCTGCCAAAGATCAGGGACAGCATGGGGCAGAAAGGCACGGGGAAGTGGACTGCCATCTCCACCCTGGAGTACGGCATA
CCCGTTACCCTCTTGGAGAAGCTGTCTTTGCTCGGTGCTTGTTATCTCTGAAGAATGAGAGAATTCAAGCTAGCAAAAAG
CTGAAGGGTCCCCAAAAGTTCCAGTTTGATGATGATAAGAAATCATTCCTGGAGGACATTCAGAAGGCCCTCTATGCTTC
CAAGATCATCTCTTATGCTCAAGGCTTTATGCTGCTAAGGCAGGCAGCCACCAAGTTTGGCTGGACCCTCAATTATGGTG
GCATCGCCCTGATGTGGAGACTGAGCTGCATCATCAGAAGTGTATTCCTAGGAAAGATAAAGGATGTATTTGATCGAAAC
AAGGAATTCCAGAACCTCCTACTGGACGACTTCTTTAAGGCAGCTGTTGAAAACTGTCAGGACTCCTGGCGGCCAGCAGT
CAGCACTGGGATCCAGACTGGCCTTCCCATACCTTGTTTTACCACTGCCCTCTCCTTCTATGACAGGTACAGACACAAGA
TGCTTCCAGCCAACCTCATTCAGGCTCAGCAGGATTAATTCAGGGCTCACACCTATGAACTCTTGGCCAAACCAGGGCAG
TTTTTCCACACCAATTGGACAGGCCACAGTAACAGTGTGTCATCCTCATCATACAATGCC

Alignment

ORF - retro_cjac_2892 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.6 %
• Parental protein coverage: 78.72 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RDLKAKGILFVGSGVSGGEEGARYGPSLMPGGNKEAWPHIKTIFQGIAAKVGTGEPCCDWVGEEGAGHFV
          R.LKAKGILFVG.GVSGGEEGA.Y.PSLMPGGNKEAWPHIKTIFQGIAAKVGTGEPCCDWV...GAGHF.
Retrocopy RHLKAKGILFVGIGVSGGEEGAWYDPSLMPGGNKEAWPHIKTIFQGIAAKVGTGEPCCDWV---GAGHFM

Parental  KMVHNGIEYGDMQLICEAYHLMKDVLGMAQDEMAQAFEDWNKTELDSFLIEITANILKFQDADGKHLLPK
          KMVH..IEYGDMQLICEAYHLMKDVL.M.QD.M.QAFEDWNKTELD.FLIEITANILKFQDAD..HLLPK
Retrocopy KMVHSRIEYGDMQLICEAYHLMKDVLAMVQDKMVQAFEDWNKTELDLFLIEITANILKFQDADSRHLLPK

Parental  IRDSAGQKGTGKWTAISALEYGVPVTLI-GEAVFARCLSSLKDERIQASKKLKGPQKFQFDGDKKSFLED
          IRDS.GQKGTGKWTAIS.LEYG.PVTL..GEAVFARCL.SLK.ERIQASKKLKGPQKFQFD.DKKSFLED
Retrocopy IRDSMGQKGTGKWTAISTLEYGIPVTLL<GEAVFARCLLSLKNERIQASKKLKGPQKFQFDDDKKSFLED

Parental  IRKALYASKIISYAQGFMLLRQAATEFGWTLNYGGIALMWRGGCIIRSVFLGKIKDAFDRNPELQNLLLD
          I.KALYASKIISYAQGFMLLRQAAT.FGWTLNYGGIALMWR..CIIRSVFLGKIKD.FDRN.E.QNLLLD
Retrocopy IQKALYASKIISYAQGFMLLRQAATKFGWTLNYGGIALMWRLSCIIRSVFLGKIKDVFDRNKEFQNLLLD

Parental  DFFKSAVENCQDSWRRAVSTGVQAGIPMPCFTTALSFYDGYRHEMLPANLIQAQRDYFGAHTYELLAKPG
          DFFK.AVENCQDSWR.AVSTG.Q.G.P.PCFTTALSFYD.YRH.MLPANLIQAQ.D.F.AHTYELLAKPG
Retrocopy DFFKAAVENCQDSWRPAVSTGIQTGLPIPCFTTALSFYDRYRHKMLPANLIQAQQD*FRAHTYELLAKPG

Parental  QFIHTNWTGHGGSVSSSSYNA
          QF.HTNWTGH..SVSSSSYNA
Retrocopy QFFHTNWTGHSNSVSSSSYNA

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	74.75 RPM
SRP051959_heart	0.02 RPM	15.49 RPM
SRP051959_kidney	0.00 RPM	30.24 RPM
SRP051959_liver	0.00 RPM	31.60 RPM
SRP051959_lung	0.02 RPM	36.57 RPM
SRP051959_lymph_node	0.02 RPM	20.11 RPM
SRP051959_skeletal_muscle	0.00 RPM	7.84 RPM
SRP051959_spleen	0.00 RPM	37.58 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2892 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2892 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2892 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005090	2 retrocopies	retro_cjac_1405, retro_cjac_2892 ,
Homo sapiens	ENSG00000142657	1 retrocopy	retro_hsap_1877,
Gorilla gorilla	ENSGGOG00000004754	2 retrocopies	retro_ggor_1374, retro_ggor_811,
Macaca mulatta	ENSMMUG00000023029	1 retrocopy	retro_mmul_1328,
Otolemur garnettii	ENSOGAG00000011164	1 retrocopy	retro_ogar_3372,