RetrogeneDB ID: retro_ogar_3372

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873806.1:196993..197890(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PGD
• Ensembl ID: ENSOGAG00000011164
• Aliases: None
• Description: phosphogluconate dehydrogenase [Source:HGNC Symbol;Acc:8891]

Sequence

>retro_ogar_3372
ATGGTGCACAATGGAATAGAGTATGGTGACATGCGGCTAATCTGTGAGGCTTACCACTTGATGAGAGATGTCCTGGGCAT
GGAGCAAAGTGAGATGGCACAGGCCTTTGAAGAGTGGAATAAGATGGAAGTAGACTCATTCCTGACTGAAATCACAGCCA
ATATTCTCAAGTTCCAAGATAACAATGGCAAATACCTGCTGCCAAAAATCAGTGACAGAGCTGGGCAGAAGGGCACCGGG
AATTGGTCGGCTATCTCCACCCTGGAATATGGCATCCCTGTCGCCCTCATTGGAGAAGCTGTCTTTGCTCGATGCTTATC
ATCTCTGAAGGATGAAAGAATTCAAGCAAGCAAAAAACTAATGGGTCCCCAAAAGACCCAGTTTGAAGGTGACAAGAAAT
CATTCCTGGAAGACATTCAAAAGGCCCTCTATGCTTCCAAGATCATCTCTTATGCCCAAGGCTTTATGCTGCTAAGACAA
GCAGCCATTGAATTTGGCTGGACCCTCAATTATGGTGGCATCACCCTGATGTGGAGAGGGAGCTGCATCATCAGGAGTGT
ATTCCTAGAAAAGATAAAGGATGCATTTGATCAAAACCCGGAACTTCAGAACCTACTACTTGACAACTTCTTTAAGTCAG
CTGTTGAAAACTGCCAGGCCTCCTGGCAGTGGGTAGTCAGTACTGGTGTCCAGGCAGGCATCCCCATGCCCTGCTTCACC
ACTGCCCTCTCCTTCTATAATGGGTACAGACATGAGATGCTACCAGCCAACCTCATCCAGGCTAAGCAGGATTACTTTGG
AGCTCATACCTATGAACTCTTAGCCAACGCGTGACAGTTTATCCACACTAACTGGACGGGCCATGGTGGCAACGTGTCCT
CCTCTTCATACAATGCT

Alignment

ORF - retro_ogar_3372 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.61 %
• Parental protein coverage: 61.9 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VAHLGERKGTEWVVVVSKVLSRDCLSIPPSILAFAFEEWNKTELDSFLIEITANILKFQDNDGKYLLPKI
          ..H.G...G..........L.RD.L....S..A.AFEEWNK.E.DSFL.EITANILKFQDN.GKYLLPKI
Retrocopy MVHNGIEYGDMRLICEAYHLMRDVLGMEQSEMAQAFEEWNKMEVDSFLTEITANILKFQDNNGKYLLPKI

Parental  KDSAGQKGTGKWTAISALEYGVPVTLIGEAVFARCLSSLKDERIQASKKLMGPQKTQFEGDKKSFLEDIR
          .D.AGQKGTG.W.AIS.LEYG.PV.LIGEAVFARCLSSLKDERIQASKKLMGPQKTQFEGDKKSFLEDI.
Retrocopy SDRAGQKGTGNWSAISTLEYGIPVALIGEAVFARCLSSLKDERIQASKKLMGPQKTQFEGDKKSFLEDIQ

Parental  KALYASKIISYAQGFMLLRQAATEFGWTLNYGGIALMWRGGCIIRSVFLGKIKDAFDRNPELQNLLLDNF
          KALYASKIISYAQGFMLLRQAA.EFGWTLNYGGI.LMWRG.CIIRSVFL.KIKDAFD.NPELQNLLLDNF
Retrocopy KALYASKIISYAQGFMLLRQAAIEFGWTLNYGGITLMWRGSCIIRSVFLEKIKDAFDQNPELQNLLLDNF

Parental  FKSAVENCQASWRRVVSTGVQAGIPMPCFTTALSFYDGYRHEMLPANLIQAQRDYFGAHTYELLANPGQF
          FKSAVENCQASW..VVSTGVQAGIPMPCFTTALSFY.GYRHEMLPANLIQA..DYFGAHTYELLAN..QF
Retrocopy FKSAVENCQASWQWVVSTGVQAGIPMPCFTTALSFYNGYRHEMLPANLIQAKQDYFGAHTYELLANA*QF

Parental  IHTNWTGHGGNVSSSSYNA
          IHTNWTGHGGNVSSSSYNA
Retrocopy IHTNWTGHGGNVSSSSYNA

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq

Otolemur garnettii was not studied using ChIP-Seq data.

EST

Otolemur garnettii was not studied using EST data.

TSS

Otolemur garnettii was not studied using FANTOM5 data.

Lab

retro_ogar_3372 was not experimentally validated.

Homology

Retrocopy orthology:

Otolemur garnettii does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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 ,