RetrogeneDB ID: retro_ggor_1374

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 18:29177088..29177695(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGGOG00000026472
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_1374
GAATCCTGCTGTGACTGGGTGGGAGATGAGGGAGCAGGCCACTTTGTGAAGATGGCGCACAACGGGACAGAGTATGGGGA
CATGCAGCTGATCTGTGAGGCATACCACCTGATGAAAGACGTGCTGGGCATGGCACAAGACAAGATGGCCCAGGCCTTTG
AGGATTGGAATAAGACAGAGCTAGACTCATTCCTGATTGAAATCACAGCCAATATTCTCAAGTTCCAAGGTGCTGATGGC
AAACACTTGCTGCCAAAGATCAGGGACAGTGCAGGGCAGAAGGGCATGGGGAAGTGGACCACCATTTCTGCCCTGGAGTA
CGGCATACCCGTCACCCTCATTGGAGAAGCTGTCTTTGCTCGGTGCCTGTCATCTCTGAAGGATGGGAGAATTCAAGCTA
GCAAAAAGCTGAAGGGTCCCCAAAAGTTCCAGTTTGATGGTGATAAGAAATCATTCCTGGAGGATATTCAGAATGTCCCT
CTACACTTCCAAGATCATCTCTTATGCTCAAGGCTTTATGCTGCTAAGGCAGGGAGCCACCGAGTTTGGCTGGACCCTCA
ATTATGGTGACATTGCCCTGATGTGGAGAGGGGGCTGCATTATTAGA

Alignment

ORF - retro_ggor_1374 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.63 %
• Parental protein coverage: 54.74 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EPCCDWVGDEGAGHFVKMVHNGIEYGDMQLICEAYHLMKDVLGMAQDEMSQAFEDWNKTELDSFLIEITA
          E.CCDWVGDEGAGHFVKM.HNG.EYGDMQLICEAYHLMKDVLGMAQD.M.QAFEDWNKTELDSFLIEITA
Retrocopy ESCCDWVGDEGAGHFVKMAHNGTEYGDMQLICEAYHLMKDVLGMAQDKMAQAFEDWNKTELDSFLIEITA

Parental  NILKFQDTDGKHLLPKIRDSAGQKGTGKWTAISALEYGVPVTLIGEAVFARCLSSLKDERIQASKKLKGP
          NILKFQ..DGKHLLPKIRDSAGQKG.GKWT.ISALEYG.PVTLIGEAVFARCLSSLKD.RIQASKKLKGP
Retrocopy NILKFQGADGKHLLPKIRDSAGQKGMGKWTTISALEYGIPVTLIGEAVFARCLSSLKDGRIQASKKLKGP

Parental  QKFQFDGDKKSFLEDI-RKALYASKIISYAQGFMLLRQAATEFGWTLNYGGIALMWRGGCIIR
          QKFQFDGDKKSFLEDI.R..LY.SKIISYAQGFMLLRQ.ATEFGWTLNYG.IALMWRGGCIIR
Retrocopy QKFQFDGDKKSFLEDI>RMSLYTSKIISYAQGFMLLRQGATEFGWTLNYGDIALMWRGGCIIR

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	0.29 RPM	35.49 RPM
SRP007412_cerebellum	0.16 RPM	20.45 RPM
SRP007412_heart	0.03 RPM	5.91 RPM
SRP007412_kidney	0.16 RPM	34.55 RPM
SRP007412_liver	0.18 RPM	13.40 RPM
SRP007412_testis	0.31 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_1374 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1374 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1877
Macaca mulatta	retro_mmul_1328

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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,