RetrogeneDB ID: retro_mdom_267

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:533260570..533262160(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000014612
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: PKLR
• Ensembl ID: ENSMODG00000017053
• Aliases: None
• Description: pyruvate kinase, liver and RBC [Source:HGNC Symbol;Acc:9020]

Sequence

>retro_mdom_267
ATGGAGAAAACATTAAGTGAAACAGATTTACCAATTAATCCAAATCAGGAATATGCTAACAAGGCTGAAAACTTTCTGGA
ATACATGTGTCGTCTGTGCATTGACTCAGAGCCCAGTGTTGCCCGAAACACTGCTATCATCTGCACCATTGGCCCAGCTT
CTCAATCTGTAGATACATTAAAAAAGATGATTAGCGCTGGAATGAATGTGGCTCGTATAAACACCTGCCATGGAAATCAA
GAGGAACACGCCATGATGATCAAAAATGTACGAACGGCTACAGACAGTTTTCTTTCTGATCCCATGTTCTATCGGCCTAT
TGCTATAGCATTGGACATAAAAGGACCATCCGTCCGGACTGGACTCATCAAGGGCAGTGAATCAGCTGAAGTAGAGCTAA
AGAAGGGCAATTCTATCAAAGTCACTTTGGATGATACATATAAGGAAAACTGCGATGAGAATATTCTGTGGGTAGACAAC
AAAAGAGTTTTCACCGACATAAAGATTGATGGCAAGATCTATGTGGACAATGGGCTCATTTGTCTGGTTGTGAGGGAGAA
AGGTAATGGTTTCCTTTTGACTGAGGTGACAAGTGGTGGAATGCTAGGCAGCAAGAAATGCTTGAACTTTCCTGGGTTGA
AAATGGACTTTGCTCTTACAACTAAGGATAAAGAAGATTTAAAGTTTGGATTAGAGCAAAAGGTAGATATGGTGTTTGCA
TCTTTCATCCAAAAGGCAGGGGATGTCCAAGAAGTCAGAAAGATACTTGGGAAAGAAGGAGAAAGCGTGTTGGTCATCAG
CAAGATTGAGAACCATGAAGGAGTTAAAAATTTTGATGAGATCCTGAAAGTCAGTGATGGCATTATGATTGCTCGGGGGG
ACCTAGGTATTGAGATCCCTCCACAAAAAGTCTTCCTTGCTCAGAAGATGATGATTGGAAGGTGTAATCTAGCTGGGAAA
CCTGTTATCTGTGCCACCCAGATGCTACAGAGCATGATTAAGAAGCCACGTCCCACTCGAGCAGAAAGCAGTGATATAGC
CAATGCTGTCCTAGATGGAGTAGATTGTGTCATGTTGTCAGGGGAGACCGCCAAAGGGGACTACCCAGTAGAATGTGTAA
AGGTCCAACACAGGATTGCCCGAGAGGCAGAGGCTGCCACCTTTCACTTGCAGTTATTTAATGAACTTGTCAACCTGGTA
CCCCACAATAAGGATTTTACTGAAATTACTGCTGTGGGTGCTGTAAAAGCATCCTTCAACTATGCCAGTGAGGCCATCAT
CGTTCTCACTGACACTGGAAAATCAGCTTATTTGATAGCCAGGTATCATCCCCGGGTCCCTATCCTTGCTGTTATTCGGG
ATGCCCAAGTTGCACGGCAGGTTAATTTGTACCGAGGCATCTTTCCTATACTGTACCTTAAACCTGTTGAAACAAAATGG
ACTGAAGATGTCGAAATAAGGATTAACTATGCCATGGATGTAGGCAAAGCTCAAGGCTTTTTCAAGAAAGATGATATGGT
CATTGTAGTAAGTGGTTGGTGTCCAGAGATAGGCTGTACCAACACTATGAATTTGCTTCCAGTTACCTAA

Alignment

ORF - retro_mdom_267 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.55 %
• Parental protein coverage: 86.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ADTFLEHLCLLDIDSEPVTARNTGIIATIGPASRSVDRLKEMIKAGMNIARLNFSHGSHEYHAESIANVR
          A..FLE..C.L.IDSEP..ARNT.II.TIGPAS.SVD.LK.MI.AGMN.AR.N..HG..E.HA..I.NVR
Retrocopy AENFLEYMCRLCIDSEPSVARNTAIICTIGPASQSVDTLKKMISAGMNVARINTCHGNQEEHAMMIKNVR

Parental  EAAESFAASPITYRPVAIALDTKGPEIRTGILQGGPEAEVKLEKGSEVRVTVNPEFRTLGNASTVWVDYP
          .A..SF...P..YRP.AIALD.KGP..RTG...G...AEV.L.KG....VT..............WVD..
Retrocopy TATDSFLSDPMFYRPIAIALDIKGPSVRTGLIKGSESAEVELKKGNSIKVTLDDTYKENCDENILWVDNK

Parental  NIVQVVQEGGFIYLDDGLISLVVKQKGQDELVTEVENGGILGSRKGVNLPGAEVDLPGLSEQDVQDLRFG
          .........G.IY.D.GLI.LVV..KG...L.TEV..GG.LGS.K..N.PG...D...L...D..DL.FG
Retrocopy RVFTDIKIDGKIYVDNGLICLVVREKGNGFLLTEVTSGGMLGSKKCLNFPGLKMDF-ALTTKDKEDLKFG

Parental  VEQGVDIVFASFIRKARDVIAIREALGLRGRGIKIVSKIENHEGVERFDEILEVSDGIMVARGDLGIEIP
          .EQ.VD.VFASFI.KA.DV...R..LG..G......SKIENHEGV..FDEIL.VSDGIM.ARGDLGIEIP
Retrocopy LEQKVDMVFASFIQKAGDVQEVRKILGKEGESVLVISKIENHEGVKNFDEILKVSDGIMIARGDLGIEIP

Parental  AEKVFLAQKMMIGRCNLAGKPVVCATQMLESMVTNARPTRAETSDVANAVLDGADCIMLSGETAKGKYPV
          ..KVFLAQKMMIGRCNLAGKPV.CATQML.SM....RPTRAE.SD.ANAVLDG.DC.MLSGETAKG.YPV
Retrocopy PQKVFLAQKMMIGRCNLAGKPVICATQMLQSMIKKPRPTRAESSDIANAVLDGVDCVMLSGETAKGDYPV

Parental  EAVKMQHAIAREAEAAIFHRQLFEELRRAIPLSRDPAEVTAIGAVEASFKCCAAAIIVLTTTGRSAQLIS
          E.VK.QH.IAREAEAA.FH.QLF.EL....P...D..E.TA.GAV.ASF.....AIIVLT.TG.SA.LI.
Retrocopy ECVKVQHRIAREAEAATFHLQLFNELVNLVPHNKDFTEITAVGAVKASFNYASEAIIVLTDTGKSAYLIA

Parental  RYRPRAVVIAVTRFAQAARQAHLFRGVFPLLYREPPAPIWSEDVDRRVQFGIENGKLRGFIRTGDLVIVV
          RY.PR....AV.R.AQ.ARQ..L.RG.FP.LY..P....W.EDV..R.......GK..GF....D.VIVV
Retrocopy RYHPRVPILAVIRDAQVARQVNLYRGIFPILYLKPVETKWTEDVEIRINYAMDVGKAQGFFKKDDMVIVV

Parental  TGWRPGSGSTSIMRVLSVS
          .GW.P..G.T..M..L.V.
Retrocopy SGWCPEIGCTNTMNLLPVT

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	0.00 RPM	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	2508.85 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_267 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_267 was not experimentally validated.

Homology

Retrocopy orthology:

Monodelphis domestica 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,