RetrogeneDB ID: retro_ggor_811

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 12:74212758..74213459(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PGD
• Ensembl ID: ENSGGOG00000004754
• Aliases: None
• Description: 6-phosphogluconate dehydrogenase, decarboxylating [Source:UniProtKB/TrEMBL;Acc:G3QQ01]

Sequence

>retro_ggor_811
ATGGCCCAAGCTGGCATTGCACTGATTGGACTGACTGTCATGGGCCAGAACTTAATATTGTGCATGAATGACCATGGCTT
CATGGCCTGTGCTTTTAATAGTACAGTCTCCAAAGTTGATGATTTCTTGGCAACAAGGCAAAGGGAACCAAAGATGTTGA
TGTTCAGTCCTTGACGGAGATGGTCTCCAAACTGAAAAAGCCACAGGCGTATCATCCCTCTTGTGAAGGCTGGTCAAGCT
GTTGATGATTTCATGAAAAAATTAGTACCATTGTTGCACACTGGTGATGTCATCATTGATGGAGGAAATTCTGAATATAG
GGATGACACAAGACGATGTAGATACCACAAGGCCAAGGAAATTTTATCAGTGGAGAGCAAAGTTAGTGCTGGAGGAAAAG
GATCCCAGTATAGCCTATCACTCATGCCAAGAGGGAACAAAAGCTGGCCCCTATCAAGACAATCTTCTAAGGCATCACAG
CAAAAGAAAGAACTGAGGAACTTTTCTCTGACTGGGTGGGAGAGGAGGGAGCAGGCCACGTTGTAAAGATGGTGTACAAT
GGGATAGAGTATGGGGATATGCAGCTGATCTGTGGGGCTTACCACCTGATGAAACATGTGCTGGGCATGGAGCAAAACAA
GATGGCACAGGATTTTAAGGATTGGAATAAGACAGAGCTCGACTCATTCTTGAATGAAATC

Alignment

ORF - retro_ggor_811 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.05 %
• Parental protein coverage: 63.69 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAQADIALIGLAVMGQNLILNMNDHGFVVCAFNRTVSKVDDFLA-NEAKGTKVVGAQSLKEMVSKLKKP-
          MAQA.IALIGL.VMGQNLIL.MNDHGF..CAFN.TVSKVDDFLA.N.AKGTK.V..QSL.EMVSKLKKP.
Retrocopy MAQAGIALIGLTVMGQNLILCMNDHGFMACAFNSTVSKVDDFLA<NKAKGTKDVDVQSLTEMVSKLKKP>

Parental  RRIILLVKAGQAVDDFIEKLVPLLDTGDIIIDGGNSEYRDTTRRCRDLKAKGILFVGSGVSGGEEGARYG
          RRII.LVKAGQAVDDF..KLVPLL.TGD.IIDGGNSEYRD.TRRCR..KAK.IL.V.S.VS.G..G..Y.
Retrocopy RRIIPLVKAGQAVDDFMKKLVPLLHTGDVIIDGGNSEYRDDTRRCRYHKAKEILSVESKVSAGGKGSQYS

Parental  PSLMPGGNKEAWP-HIKTIFQGIAAKVGTGEPCCDWVGDEGAGHFVKMVHNGIEYGDMQLICEAYHLMKD
          .SLMP.GNK..WP..IKTIF.GI.AK..T.E...DWVG.EGAGH.VKMV.NGIEYGDMQLIC.AYHLMK.
Retrocopy LSLMPRGNK-SWP<PIKTIF*GITAKERTEELFSDWVGEEGAGHVVKMVYNGIEYGDMQLICGAYHLMKH

Parental  VLGMAQDEMSQAFEDWNKTELDSFLIEI
          VLGM.Q..M.Q.F.DWNKTELDSFL.EI
Retrocopy VLGMEQNKMAQDFKDWNKTELDSFLNEI

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_prefrontal_cortex	0.00 RPM	35.49 RPM
SRP007412_cerebellum	0.00 RPM	20.45 RPM
SRP007412_heart	0.00 RPM	5.91 RPM
SRP007412_kidney	0.00 RPM	34.55 RPM
SRP007412_liver	0.00 RPM	13.40 RPM
SRP007412_testis	0.00 RPM	69.41 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_811 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_811 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,