RetrogeneDB ID: retro_ogar_1705

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873562.1:6742543..6743824(+)
• 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_1705
TTTGCATCTGACCCCATTCTCTACCAGCCAGTTGCTGTGGCTCTGGACACGAAAGCACCTGAGATTCGAACTGGGCTCAT
CAAGGGCAGCAGCACCGCAGAGGTAGAGCTGAAGAAAGGAGCCACTCTCAAGATCACGTTGGACAATGCCTACATGGAGA
AGTGTGACGAGAACATCTTGTGGCTGGACTACAAGAACATCTGTAAAGTGGTGGAGGTGGGCAGCAAGATCCATGTGGAT
GATGGACTGATTTCCCTGCTGGTGAAGCAGAAAGGTGGTGACTTCCTGGTGACAGAGGTGGAAAATGGCAGCAGCAAGAA
GGGTGTAAACATTCTCAGGGCTGCTGTGGACCTGCCTGCTGTATCAGAAAAGGATATCCAGGACCTGAAGTTTGGGGTAG
AGCAGGATATAGATATGTTTGCATCTTTCATCCACAAGGTGTCTGATGTCCATGATGTCAGGAAGGTCCTGGGAGAGAAA
GGAAAGAACATCAAGATAATCAGCAAAATCGAGAATCTTGAGGGAGTTCGGAGGTTTGATGAGATCCTGGAGGCCAGTGA
TGGTATCATGGTGGCTCGTGGTGACCTAGGCATTGAGATTCCTGCAGAGAAGGTCTTTCTTGCTCAGAAGATGATAATTG
GGCGGTGCAACCGAGCTGAGATGCCTGTCATCTGTGCCATGCAGCTGCTGGAGAGCATGATCAAGAAGCCTCACCCCACC
TGCTTAGAGGGCAGCAATGTGGCCAATGCAGTCCTGGACGGAGCTGACTGCATCATGCTGTCTAGAGAAACAGCCAAAGG
GGACTACCCTCTGGAAGCTGTTCACATGCAGCTCCTGATTGCCCCTGAGGCAGAGGCTGCCATCTACCACTTGCAATTAT
TTGAGGAACTCCACTGCCTGGCGCCCATTACCAGCAACCCCACAGAAGCTGCTGCCATAGGCACCATGGAGGCCCCCTTC
AATTGCTGCAGTGGGGGCCATAATAGTCCTCACAAAGTCTGGCAGGTCAGCTCACCAGGTGGTCAGATACTGCCCACGTG
CCCCCATCATTTCTATGACACGGAATCCCTAGACAGCTTGCCAGGCCCACCTATACCATGGCATATTCCTGTCTTATGCA
AGGACCCAGTCCAGGAAGCCTGGGCTGAAGATGTGGACCTCTGGGTGAACTTGGCCATGGATGTTGGAAAGGCCCGAGGC
TTCTTCAAGTCAGGAGATGTAGTCATTGTGCTGACTGGGTGGCGCCCTGGCTCTAGCTTCACCAACACCATGTGTGTAGT
G

Alignment

ORF - retro_ogar_1705 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.51 %
• Parental protein coverage: 74.91 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FATSAFSYRPVAIALDTKGPEIRTGTLMGGSDSEVELVKGSQVLVTVDPAFQMRGDENTVWVDYPNIVQV
          FA.....Y.PVA.ALDTK.PEIRTG...G.S..EVEL.KG.....T.D.A.....DEN..W.DY.NI..V
Retrocopy FASDPILYQPVAVALDTKAPEIRTGLIKGSSTAEVELKKGATLKITLDNAYMEKCDENILWLDYKNICKV

Parental  VPVGGRIYIDDGLISLV----GPEGLVTQVENGGILGNRKGVNLPRIQVDLPGLSEQDVRDLRFGVEHGV
          V.VG..I..DDGLISL.....G...LVT.VENG......KGVN..R..VDLP..SE.D..DL.FGVE...
Retrocopy VEVGSKIHVDDGLISLLVKQKGGDFLVTEVENGS---SKKGVNILRAAVDLPAVSEKDIQDLKFGVEQDI

Parental  DIIFASFVRKASDVAAIRAVLGPEGQNIKIISKIENHEGVKSFDEILEVSDGIMVARGDLGIEIPEEKVF
          D..FASF..K.SDV...R.VLG..G.NIKIISKIEN.EGV..FDEILE.SDGIMVARGDLGIEIP.EKVF
Retrocopy DM-FASFIHKVSDVHDVRKVLGEKGKNIKIISKIENLEGVRRFDEILEASDGIMVARGDLGIEIPAEKVF

Parental  LAQKMMIGRCNLAGKPVICATQMLESMITKPRPTRAETSDVANAVLDGADCIMLSGETAKGHFPVEAVKM
          LAQKM.IGRCN.A..PVICA.Q.LESMI.KP.PT..E.S.VANAVLDGADCIMLS.ETAKG..P.EAV.M
Retrocopy LAQKMIIGRCNRAEMPVICAMQLLESMIKKPHPTCLEGSNVANAVLDGADCIMLSRETAKGDYPLEAVHM

Parental  QHAIAREAEAAVYHQQLFEELRRAAPLSRDPTEVTAIGAVEAAFKCCA-AAIIVLTTTGRSAQLLSRYRP
          Q..IA.EAEAA.YH.QLFEEL...AP....PTE..AIG..EA.F.CC...AIIVLT..GRSA....RY.P
Retrocopy QLLIAPEAEAAIYHLQLFEELHCLAPITSNPTEAAAIGTMEAPFNCCS>GAIIVLTKSGRSAHQVVRYCP

Parental  RAAVIAVTRSAQAARQIHLCRGVF-PLLYREHPEAVWADDVDRRVQFGIESGKLRGFLCVGDLVIVVTGW
          RA..I..TR....A.Q.HL..G.F.P.L........WA.DVD..V......GK.RGF...GD.VIV.TGW
Retrocopy RAPIISMTRNP*TACQAHLYHGIF<PVLCKDPVQEAWAEDVDLWVNLAMDVGKARGFFKSGDVVIVLTGW

Parental  RPGSGYTNIMRVL
          RPGS..TN.M.V.
Retrocopy RPGSSFTNTMCVV

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_1705 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,