RetrogeneDB ID: retro_ogar_1590

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873554.1:4774909..4776093(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PKLR
• Ensembl ID: ENSOGAG00000028418
• Aliases: None
• Description: pyruvate kinase, liver and RBC [Source:HGNC Symbol;Acc:9020]

Sequence

>retro_ogar_1590
TACTGGCCAGTTGCTGTGGCTCTGGACACAAAAGGACCTGAGATTCGAACTGGGCTCATCAAGGGCAGTGGCACTATGGA
GGTGGAGCTGAAGAAAGGAGCCACATTGGACAACGCCTGCATGGAGAAGTGTGATGAGAACATCTTGTGGCTGGACTACA
AGAACATCTGCAAAGTGGTGGAGGTGGGCAGCAAGATCCATGTGGATGATGGACTTATTTCCCTGCTGGTGAAGCAGAAA
GGTGGTGACTTCCTGGTGACAGAGGTGGAAAATGGTGGCTCCTTGGGCAGCAAGAAGGGTGTAAACCTTCCAGGGGCTGC
TGTGGACCTGCCTGCTATATCAGAAAAGGACATCCAGGACCTGAAGTTTGGGGTAGAGCAGGATGTAGATGTGGTGCTTG
CATCTTTCATCTGCAAGGCATCTGATGTCCATGAAATCAGGAAGGTCCTGGGAGTGAAAGGAAAGAACATCAAGATAATC
AGCAAAATTGAGAATCTTGAGGGAGTTCAGAGATTTGACGAGATCCTGGAGGCCAGTGATGGTATCATGGTGGGTCATGG
TGACCTAGGCATTGAGATTCCTGCAGAGAAGGACTTCCTTGCTCAGAAGATGACGATTGGGCAGTGCAACTGAGCTGGGA
AGGCTGTCATCTGTGCCACACAGATGCTGGAGAGCATGATCAAGAAGCCTCGCCCCACCCGGGCAGAGGGCAGCCATGTG
GCCAATGCAGTCCTAGACAGAGCTGACTGCATCATGCTGTCTGGAGAAATAGCCAAAGGGGACTACCCTCTGGAAGCTGT
TCGCATGCAGCACCTAATTGCCCATGAGGCAGAGGCTGCCATCTACCACTTGCAATTATTTGAGGAACTCCGCTACCTGG
CACCCATTACCAGTGACCCCACAGAAGCTGCTGCCGTAGGCGCTGTAGAGGCCTCCTTCAAGTGCTGCAGTGGGGCCATA
ATCGTCCTCATCAAGTCTGGCAGGTCAGCTCACCAGGTGGCCAGATACCGCCCACATGCCCTCATCATTACTGTGACATG
GAATCCCCAGACAGCTTGCCAGGCCCACCTATACCATGGCATATTCCTGTCTTATGCAAGGACCCAGTTCAGGAAGCCTG
GGCTGAGGATGTGGACCTCCGGGTGAACTTGGCCATGAATGTTGGAAAGGCCCAAGGCTTCGTC

Alignment

ORF - retro_ogar_1590 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64. %
• Parental protein coverage: 69.3 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YRPVAIALDTKGPEIRTGTLMGGSDSEVELVKGSQVLVTVDPAFQMRGDENTVWVDYPNIVQVVPVGGRI
          Y.PVA.ALDTKGPEIRTG...G....EVEL.KG.....T.D.A.....DEN..W.DY.NI..VV.VG..I
Retrocopy YWPVAVALDTKGPEIRTGLIKGSGTMEVELKKGA----TLDNACMEKCDENILWLDYKNICKVVEVGSKI

Parental  YIDDGLISLV----GPEGLVTQVENGGILGNRKGVNLPRIQVDLPGLSEQDVRDLRFGVEHGVDIIFASF
          ..DDGLISL.....G...LVT.VENGG.LG..KGVNLP...VDLP..SE.D..DL.FGVE..VD...ASF
Retrocopy HVDDGLISLLVKQKGGDFLVTEVENGGSLGSKKGVNLPGAAVDLPAISEKDIQDLKFGVEQDVDVVLASF

Parental  VRKASDVAAIRAVLGPEGQNIKIISKIENHEGVKSFDEILEVSDGIMVARGDLGIEIPEEKVFLAQKMMI
          ..KASDV..IR.VLG..G.NIKIISKIEN.EGV..FDEILE.SDGIMV..GDLGIEIP.EK.FLAQKM.I
Retrocopy ICKASDVHEIRKVLGVKGKNIKIISKIENLEGVQRFDEILEASDGIMVGHGDLGIEIPAEKDFLAQKMTI

Parental  GRCNLAGKPVICATQMLESMITKPRPTRAETSDVANAVLDGADCIMLSGETAKGHFPVEAVKMQHAIARE
          G.CN.AGK.VICATQMLESMI.KPRPTRAE.S.VANAVLD.ADCIMLSGE.AKG..P.EAV.MQH.IA.E
Retrocopy GQCN*AGKAVICATQMLESMIKKPRPTRAEGSHVANAVLDRADCIMLSGEIAKGDYPLEAVRMQHLIAHE

Parental  AEAAVYHQQLFEELRRAAPLSRDPTEVTAIGAVEAAFKCCAAAIIVLTTTGRSAQLLSRYRPRAAVIAVT
          AEAA.YH.QLFEELR..AP...DPTE..A.GAVEA.FKCC..AIIVL...GRSA....RYRP.A..I.VT
Retrocopy AEAAIYHLQLFEELRYLAPITSDPTEAAAVGAVEASFKCCSGAIIVLIKSGRSAHQVARYRPHALIITVT

Parental  RSAQAARQIHLCRGVF-PLLYREHPEAVWADDVDRRVQFGIESGKLRGFL
          ...Q.A.Q.HL..G.F.P.L........WA.DVD.RV......GK..GF.
Retrocopy WNPQTACQAHLYHGIF<PVLCKDPVQEAWAEDVDLRVNLAMNVGKAQGFV

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_1590 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 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000017053	1 retrocopy	retro_mdom_267,
Otolemur garnettii	ENSOGAG00000028418	3 retrocopies	retro_ogar_1590 , retro_ogar_1705, retro_ogar_522,