RetrogeneDB ID: retro_ogar_3101

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873715.1:1503224..1504315(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000003173
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PSMC6
• Ensembl ID: ENSOGAG00000010011
• Aliases: None
• Description: proteasome (prosome, macropain) 26S subunit, ATPase, 6 [Source:HGNC Symbol;Acc:9553]

Sequence

>retro_ogar_3101
CTTAAGGAGTTAAGGGAACAATTAAATAACTTACCAAACAGTATGAAAAGTTCGAAAATGATCTGAAGGCCCTACAAAGT
GTTGGGCAGATTGTGGGTGAAGTGCTTAAATAATTAACTAAAGAAAAATTCATTGTTAAAGCTACAAATGGACCAAGATA
TGCTGTGGGTTGTTGTAGACAGCTTAACAAAAGTAAGCTGAAGCCAGAAACAAGAGTTGCTTTGTATATGATGACCCTAA
CCGTCACAAGACATTTGCCCAGAGAGGTGGATCACCTAGTTTACAACATGTCTCAAGAAGACCTGGGGAATGTTTCTTAT
TCTGAGATTGGAAGATTATCAAAACAGATCCGGAAATTAAGAGAGGAGCTAGAATTACCTCTTACAAACCCAGAATTATT
TCAGTGTGTAGGAATAACACCTCCAAAAGGCTATTTGTTATATGGAACACCAGGCACAGGGAAGACACTCTTGGCATGCA
CTGTTACTAGCCAGTTGGACTGTAATTTCTTAAAGGTTGTATCTAGTCCTATTGTAGATAAGTACATTGGTGAAAGTGCT
TGTTTGATCAGAGAAATGTTTAATTATGCCAGGGACCATCAGCCGTGAATCATTTTTATGGATGAAGTAGATGCTATTGG
TGATAGTCGGTTTTCTGAGGGTACTTCAGCTGACAGAGAAATTCAGAGAACTTTAATGGAGTTACTGAATCAAATGGCTG
GATTTGATACTCTGCCTAGCGTTAAAATGATCATGGCTACAAAGAGACCACATACACTGCATCTTGCTTTACTACATCCA
GGAAGATTAGATAGAAAAATACATATTGATTTGCCAAATGAACAAGCAAGATTAGACATATTGAAAATCCATGCAGGTCC
CATTACAAAGCATGGAGAAATAGATTATGAAGCAATTGTGACGCTTTCAGATGGCTTCAATGGGGCAGACCTGAGAAATG
TTTGTCCTGAGGCAGGTATGTTTGCAATTCGTGCTGATCATGATTTTGTAGTACAGGAAGACTTCATGAAAGCAGTCAGG
AAAGTGGCTGATTCTAAGAAGCTGGAGTCTAAATTAGGCTACAAACCTGTG

Alignment

ORF - retro_ogar_3101 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.4 %
• Parental protein coverage: 93.57 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LKELREQL-KELTKQYEKSENDLKALQSVGQIVGEVLKQLTEEKFIVKATNGPRYVVGCRRQLDKSKLKP
          LKELREQL.K.LTKQYEK.ENDLKALQSVGQIVGEVLK.LT.EKFIVKATNGPRY.VGC.RQL.KSKLKP
Retrocopy LKELREQL<K*LTKQYEKFENDLKALQSVGQIVGEVLK*LTKEKFIVKATNGPRYAVGCCRQLNKSKLKP

Parental  GTRVALDMTTLTIMRYLPREVDPLVYNMSHEDPGNVSYSEIGGLSEQIRELREVIELPLTNPELFQRVGI
          .TRVAL.M.TLT..R.LPREVD.LVYNMS.ED.GNVSYSEIG.LS.QIR.LRE..ELPLTNPELFQ.VGI
Retrocopy ETRVALYMMTLTVTRHLPREVDHLVYNMSQEDLGNVSYSEIGRLSKQIRKLREELELPLTNPELFQCVGI

Parental  IPPKGCLLYGPPGTGKTLLARAVASQLDCNFLKVVSSSIVDKYIGESARLIREMFNYARDHQPCIIFMDE
          .PPKG.LLYG.PGTGKTLLA..V.SQLDCNFLKVVSS.IVDKYIGESA.LIREMFNYARDHQP.IIFMDE
Retrocopy TPPKGYLLYGTPGTGKTLLACTVTSQLDCNFLKVVSSPIVDKYIGESACLIREMFNYARDHQP*IIFMDE

Parental  IDAIGGRRFSEGTSADREIQRTLMELLNQMDGFDTLHRVKMIMATNRPDTLDPALLRPGRLDRKIHIDLP
          .DAIG..RFSEGTSADREIQRTLMELLNQM.GFDTL..VKMIMAT.RP.TL..ALL.PGRLDRKIHIDLP
Retrocopy VDAIGDSRFSEGTSADREIQRTLMELLNQMAGFDTLPSVKMIMATKRPHTLHLALLHPGRLDRKIHIDLP

Parental  NEQARLDILKIHAGPITKHGEIDYEAIVKLSDGFNGADLRNVCTEAGMFAIRADHDFVVQEDFMKAVRKV
          NEQARLDILKIHAGPITKHGEIDYEAIV.LSDGFNGADLRNVC.EAGMFAIRADHDFVVQEDFMKAVRKV
Retrocopy NEQARLDILKIHAGPITKHGEIDYEAIVTLSDGFNGADLRNVCPEAGMFAIRADHDFVVQEDFMKAVRKV

Parental  ADSKKLESKLDYKPV
          ADSKKLESKL.YKPV
Retrocopy ADSKKLESKLGYKPV

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_3101 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 12 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007126	2 retrocopies	retro_cjac_204, retro_cjac_3221,
Cavia porcellus	ENSCPOG00000009477	1 retrocopy	retro_cpor_47,
Homo sapiens	ENSG00000100519	2 retrocopies	retro_hsap_1022, retro_hsap_4059,
Gorilla gorilla	ENSGGOG00000002152	2 retrocopies	retro_ggor_2727, retro_ggor_808,
Macropus eugenii	ENSMEUG00000007084	3 retrocopies	retro_meug_1700, retro_meug_2090, retro_meug_923,
Monodelphis domestica	ENSMODG00000014500	1 retrocopy	retro_mdom_438,
Nomascus leucogenys	ENSNLEG00000012518	2 retrocopies	retro_nleu_559, retro_nleu_900,
Otolemur garnettii	ENSOGAG00000010011	1 retrocopy	retro_ogar_3101 ,
Pongo abelii	ENSPPYG00000005820	2 retrocopies	retro_pabe_3334, retro_pabe_858,
Pan troglodytes	ENSPTRG00000006352	2 retrocopies	retro_ptro_2752, retro_ptro_699,
Rattus norvegicus	ENSRNOG00000007203	1 retrocopy	retro_rnor_1480,
Tursiops truncatus	ENSTTRG00000003880	1 retrocopy	retro_ttru_117,