RetrogeneDB ID: retro_mmul_1328

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 18:24898549..24899578(+)
• Located in intron of: ENSMMUG00000032550

Retrocopy information

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

Parental gene information

• Parental gene symbol: PGD
• Ensembl ID: ENSMMUG00000023029
• Aliases: None
• Description: 6-phosphogluconate dehydrogenase, decarboxylating [Source:UniProtKB/TrEMBL;Acc:F6VFM9]

Sequence

>retro_mmul_1328
GCCCAAGCTGACATCATGCTGATCTGATTGGCAGTCATGGACCAGAACTTAATTCTGAACATGAATGACCACAGTTTTGT
GGTCTGTGCTTTTAATACGACTGTCTCCAAAGTGGATGATTTCTTGGCCAGTGAAGCAAAGGGAACCAAAGTGGTGGGTG
CCCAGTCCCTGAAAGAGATGGTCTCCAAGCTGAAGAAGCCCTGGCAGATCATCCTCCTGGTGAAGGCCAGGCAAGCTGGG
GATGATTTCATCAAAAAACTGGTACCATTGTTGGACACTGGTGACATCATCATTGATGGAGGAGATTCTGAATATAGGGA
CACCACAAGACGGTGCCAAGACCTCAAGGCCAAGGGAATTTTATTTGTGGGGAGCGGAGTCAGTGGTGGAGAGAAAGGGG
CCCGGTATGGCCCATCGCTCATGCCAGGAGGGAACGAAGAAGCGTGGCCCCACATCAAGACCATCTGCCAAGGCATTGCT
GCAAAAGTAGGAACTGGAGAGCCCTGCTGTGACTGGGTGGGAGATGAGGCAGCAGGCCACTTCGTGAAGATGGTGCACAA
CGGGATAGAGTACGGGGACGTGCTGATGATCTGTGAGGCATACCACCTGATGAAAGACGTGCTGGGCATGGCGTGGGACA
CGATGGCCCAGGCCTTTGAGGATTGGAATAAGACAGAGCTAGACTCATTCCTGATTGAAATCACAGCCAATATTCTCAAG
TTCCAAAATGCTGATGGCAAATGCTTGCTGCCAAAGATCAGGGACAGTGCGGGGCAGAAGGGCATGGGGAAGTGGACCAC
CATCTCCGCCCTGGAGTACGGTGTACCCGTCACCCTCATTGGAGAAGCTGTCTTTGCTCAGTGCCTGTCATCTCTGAAGA
ATGAGAGAATTCAAGCTAGCAAAAAGCTGAAGGGTCCCCAAAAGTTCCAGTTTGATGGTGATAAGAAATCATTCCTGGAG
GACATTTGGAAGGCCCTCTACACTTCCAAGATCATCTCTTATGCTCAAGGCTTTATGTTGCTAAGGCAG

Alignment

ORF - retro_mmul_1328 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.86 %
• Parental protein coverage: 71.13 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SRADIALIGLAVMGQNLILNMNDHGFVVCAFNRTVSKVDDFLANEAKGTKVVGAQSLKEMVSKLKKPRRI
          ..ADI.LI.LAVM.QNLILNMNDH.FVVCAFN.TVSKVDDFLA.EAKGTKVVGAQSLKEMVSKLKKP..I
Retrocopy AQADIMLI*LAVMDQNLILNMNDHSFVVCAFNTTVSKVDDFLASEAKGTKVVGAQSLKEMVSKLKKPWQI

Parental  ILLVKAGQAVDDFIEKLVPLLDTGDIIIDGGNSEYRDTTRRCRDLKAKGILFVGSGVSGGEEGARYGPSL
          ILLVKA.QA.DDFI.KLVPLLDTGDIIIDGG.SEYRDTTRRC.DLKAKGILFVGSGVSGGE.GARYGPSL
Retrocopy ILLVKARQAGDDFIKKLVPLLDTGDIIIDGGDSEYRDTTRRCQDLKAKGILFVGSGVSGGEKGARYGPSL

Parental  MPGGNKEAWPHIKTIFQGIAAKVGTGEPCCDWAKVGDEGAGHFVKMVHNGIEYGDMQLICEAYHLMKDVL
          MPGGN.EAWPHIKTI.QGIAAKVGTGEPCCDW..VGDE.AGHFVKMVHNGIEYGD...ICEAYHLMKDVL
Retrocopy MPGGNEEAWPHIKTICQGIAAKVGTGEPCCDW--VGDEAAGHFVKMVHNGIEYGDVLMICEAYHLMKDVL

Parental  GMAQDEMAQAFEDWNKTELDSFLIEITANILKFQDTDGKHLLPKIRDSAGQKGTGKWTAISALEYGVPVT
          GMA.D.MAQAFEDWNKTELDSFLIEITANILKFQ..DGK.LLPKIRDSAGQKG.GKWT.ISALEYGVPVT
Retrocopy GMAWDTMAQAFEDWNKTELDSFLIEITANILKFQNADGKCLLPKIRDSAGQKGMGKWTTISALEYGVPVT

Parental  LIGEAVFARCLSSLKDERIQASKKLKGPQKFQFDGDKKSFLEDIRKALYASKIISYAQGFMLLRQ
          LIGEAVFA.CLSSLK.ERIQASKKLKGPQKFQFDGDKKSFLEDI.KALY.SKIISYAQGFMLLRQ
Retrocopy LIGEAVFAQCLSSLKNERIQASKKLKGPQKFQFDGDKKSFLEDIWKALYTSKIISYAQGFMLLRQ

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
SRP007412_brain	1.34 RPM	27.34 RPM
SRP007412_brain_prefrontal_cortex	0.48 RPM	32.37 RPM
SRP007412_cerebellum	1.16 RPM	26.93 RPM
SRP007412_heart	1.18 RPM	28.80 RPM
SRP007412_kidney	2.70 RPM	71.36 RPM
SRP007412_liver	1.50 RPM	63.26 RPM
SRP007412_testis	1.43 RPM	37.39 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1328 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1328 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1328 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1877
Gorilla gorilla	retro_ggor_1374

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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,