RetrogeneDB ID: retro_cjac_1405

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 15:61509265..61510672(-)
• 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_1405
ATGGGCCAGAACTTAATTTTGAACATGAATGACCACTGCTTTGTGGTCTGTGCTTTTAATAGGACTGACTCCAAAGTTGA
TGATTTCTTGGCCAATGAGGCAAAGGGAACCAAAGTGGTGGGTGCTCAGTCCCTGAAGGAGATGGTCTCCAAGCTGAAGA
AGCCCCGGTAGATCATCCTCCTGGTGAAGGCTGGGCAAGCGGTTGATGATTTCATTGAAAAATTGGTACCATTGTTGGAC
ACTGGTGACATCATCATTGATGGAGGAAATTCTGAATATAGGGACACCACAAGATGGTAGCGAGACCTCGAGGCCAAGGG
AATTTTATTTGTGGGGAGTGGAGTCAGTGGCGGAGAGGAAAGAGCCCAGGATGGCCCATCAGTCATGCCAGGAGGGAACA
AAGAAGCATGACCCCACATCAAGACCATCTTCCAAGGCATCGCTGCAAAAGTAGGAACTGGAGAACCCTGCTGTGACTGG
GTGGGAGAAGAGGGAGCAGGCCACTTTGTGAAGATGGTGCACAACGGGATAGAGTATGGGACATGCAGCTGATCTGCGAG
GCGTACCACCTGATGAAAGACGTGCTAGGCATGGAGCAGGACGAGATGGTGAAGGCCTTTGAAGATTGGAACAAGAAAGA
GCTAGATTCATTCCTGATTGAAATCATAGCCAATATTCTCAAGTTCCAAGATGCCGATGGCAAACATCTGCTGCCAAAGA
TCAGGGACAGTGCAGGGCAGAAGGGCACAGGGAAGTGGACCGCCATCTCTGCCCTGGAGTACGGTGTACCCGTCACCCTC
ATTGGAGAAACTGTCTTTGCTTGGTGCTTATCATCTCTGAAGGATGAGAGAATTCAAGCTAGCAAAAAGCTGAAGGGTCC
CCAAAAGTTCCAGTTTGATGGTGATAAGAAATCATTCCTGGAGGACATTTGGAAGGCTCTCTATGCTTCCAAGATCATCT
CTTATGCTCAAGGCTTTATGCTGCTAAGGCAGGCAGCCACCGAATTTGGCTGGACCCTCAATTATGGTGGCATTGCCCTG
ATGTGGAGAGGGGGCTGCATCATTGGAAGTGTATTCCTAGGAAAGATAAAGGATGAATTTGATCAAAACCCAGAACTCCA
GAACCTCCTACTGGATGACTTCTTTAAGTCAGCTTTTGAAAACTGCCAGGACTCCTGGAGGCGGGCAGTCAGCACTGGGG
TCCCAGCTGGCATTCCCATGCCCTGTTTTACCACTGCCCTCTCCTTCTATGACGGGTACAGACATGAGATGCTTCCAGCC
AAACTCATCCAGGCTCAGCGGGATTACTTTGGGGCCCACATCTATGAACTCTTGGCCAAACCAGGCAGTTTATCTGCACC
AATTGGACAGGCATGGTGGCAGTGTGTCATCCTCGTCATACAATGCC

Alignment

ORF - retro_cjac_1405 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.66 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MGQNLILNMNDHGFVVCAFNRTVSKVDDFLANEAKGTKVVGAQSLKEMVSKLKKPRRIILLVKAGQAVDD
          MGQNLILNMNDH.FVVCAFNRT.SKVDDFLANEAKGTKVVGAQSLKEMVSKLKKPR.IILLVKAGQAVDD
Retrocopy MGQNLILNMNDHCFVVCAFNRTDSKVDDFLANEAKGTKVVGAQSLKEMVSKLKKPR*IILLVKAGQAVDD

Parental  FIEKLVPLLDTGDIIIDGGNSEYRDTTRRCRDLKAKGILFVGSGVSGGEEGARYGPSLMPGGNKEAWPHI
          FIEKLVPLLDTGDIIIDGGNSEYRDTTR..RDL.AKGILFVGSGVSGGEE.A..GPS.MPGGNKEA.PHI
Retrocopy FIEKLVPLLDTGDIIIDGGNSEYRDTTRW*RDLEAKGILFVGSGVSGGEERAQDGPSVMPGGNKEA*PHI

Parental  KTIFQGIAAKVGTGEPCCDWVGEEGAGHFVKMVHNGIEYG-DMQLICEAYHLMKDVLGMAQDEMAQAFED
          KTIFQGIAAKVGTGEPCCDWVGEEGAGHFVKMVHNGIEYG.DMQLICEAYHLMKDVLGM.QDEM..AFED
Retrocopy KTIFQGIAAKVGTGEPCCDWVGEEGAGHFVKMVHNGIEYG<DMQLICEAYHLMKDVLGMEQDEMVKAFED

Parental  WNKTELDSFLIEITANILKFQDADGKHLLPKIRDSAGQKGTGKWTAISALEYGVPVTLIGEAVFARCLSS
          WNK.ELDSFLIEI.ANILKFQDADGKHLLPKIRDSAGQKGTGKWTAISALEYGVPVTLIGE.VFA.CLSS
Retrocopy WNKKELDSFLIEIIANILKFQDADGKHLLPKIRDSAGQKGTGKWTAISALEYGVPVTLIGETVFAWCLSS

Parental  LKDERIQASKKLKGPQKFQFDGDKKSFLEDIRKALYASKIISYAQGFMLLRQAATEFGWTLNYGGIALMW
          LKDERIQASKKLKGPQKFQFDGDKKSFLEDI.KALYASKIISYAQGFMLLRQAATEFGWTLNYGGIALMW
Retrocopy LKDERIQASKKLKGPQKFQFDGDKKSFLEDIWKALYASKIISYAQGFMLLRQAATEFGWTLNYGGIALMW

Parental  RGGCIIRSVFLGKIKDAFDRNPELQNLLLDDFFKSAVENCQDSWRRAVSTGVQAGIPMPCFTTALSFYDG
          RGGCII.SVFLGKIKD.FD.NPELQNLLLDDFFKSA.ENCQDSWRRAVSTGV.AGIPMPCFTTALSFYDG
Retrocopy RGGCIIGSVFLGKIKDEFDQNPELQNLLLDDFFKSAFENCQDSWRRAVSTGVPAGIPMPCFTTALSFYDG

Parental  YRHEMLPANLIQAQRDYFGAHTYELLAKPG-QFIHTNWTG-HGGSVSSSSYNA
          YRHEMLPA.LIQAQRDYFGAH.YELLAKPG.QFI.TNWTG.HGGSVSSSSYNA
Retrocopy YRHEMLPAKLIQAQRDYFGAHIYELLAKPG<QFICTNWTG<HGGSVSSSSYNA

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	0.04 RPM	74.75 RPM
SRP051959_heart	0.09 RPM	15.49 RPM
SRP051959_kidney	0.13 RPM	30.24 RPM
SRP051959_liver	0.11 RPM	31.60 RPM
SRP051959_lung	0.07 RPM	36.57 RPM
SRP051959_lymph_node	0.02 RPM	20.11 RPM
SRP051959_skeletal_muscle	0.00 RPM	7.84 RPM
SRP051959_spleen	0.13 RPM	37.58 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1405 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1405 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1405 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,