RetrogeneDB ID: retro_ptri_3

Retrocopy location

• Organism: Western balsam poplar (Populus trichocarpa)
• Coordinates: 17:14425068..14427453(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: POPTR_0017s14340
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: POPTR_0006s12740
• Aliases: None
• Description: None

Sequence

>retro_ptri_3
ATGGGAGACCAGGCAGGCACAAACAAAAGAAAGAGAGATTTTAGTGATTCAATTATGGAGCGCAATAAGAAGGCACCCAA
CAGGCTTCTTGTTGATGAAGCCATTAACGATGACAACTCTGTCATCACGCTCAATCCAGCTACAATGGAGCAACTTGATA
TTTTCCGCGGGGATAGCTTGTTGATCAAGGGAAAGAAGAGGAGGGATACAGTTTGTATTGCCCTAGCTGATGATCGTTGC
GATCAGCCCAAGATTCTGATGAATAAGGTTGTGAGGTCAAACTTAAGGGTCAGGCTTGGCGATATGGTTTCGGTGCAGCT
ATGTCATAACTTGCAGTATGGCAAGAGGGTTCACATTCTGCCTTTGGATGACACAGTTGATGGCCTTAGCGGTAGTCTGT
TTGATGCCTACTTGAAGCCTTACTTTAAGGATTCTCACCGTCCTGTCAGGAAAGGAGATCTTTTCCTTGTCAGAGGAGGA
ATGAGGAGTGTGGAGTTTAAGGTCATTGAGACCGATCCTGCTGAGTACTGTGTGGTTGAGCCTGATACGGAGATCTTCTG
TGAAGGGGAAGCTGTGAAGAGGGAAGATGAGGAAAGGCTTGATGGTATTGGCTATGATGATCTTGGTGGCGTTAGGAAAC
AATTGGCACTAATCAGGGAGATGGTCGAACTGCCATTAAGGTTTCCACAACTTTTCAAGACCATTGGTGTGAAGCCACCG
AGAGGAATTCTGCTTTATGGTCCTCCTGGAACAGGTAAAACATTGATAGCAAGGGCTATTGCTAATGAAACTGGGGCTTT
CTTCTTTTGTATCAATGGACCAGAAATCATGTCCAAGATGGCAGGAGAGAGTGAGCAAAATCTGAGAAAAGCTTTTGAAG
AAGCTGAAAAGAATGCTCCTGCAATTGTATTTATTGATGAGATTGATTCAATTGCTCCCAAACGTGAGAAAACTGGTGGG
GAAGTAGAGAGACGAATCGTTTCACAACTACTGACTCTTATGGATGGGCTAAAGGCTCGTGCCCATGTTATTGTTATAGG
AGCTACAAACAGGCCTAACAGTCTAGACCCTGCATTGAGGAGGTTTGGAAGGTTTGACAAAGAAATAGATATTGGTGTTC
CAGATGAAGTTGGTCGCCTTGAGGTTCTTCGTGTCCATACAAAGAAAATGAAGCTCTCTGAAGATGTAGACTTGGAAAAA
GTAGCCAAAGGAACTCAGGGGTATGTTGGTGCAGATCTTGCAGCTCTTTGCAGCGAATCTGCCCTACAATGCATTAGGGA
AAAGATGGGCATCATTGATTTGGAAGATGATACGATTGATGCTGAGGTTCTTAATTCCATGGCCGTTACAAATGAGCACT
TCAGCATTGCTCTCGGAACCAGCAATCCTTCTGCTCTTCGTGAAACCATTGTAGAAGTTCCCAATGTTAGATGGGAGGAT
ATTGGTGGTCTTGAGAAGGTCAAGATGGAGCTTCAAGAGACTGTTCAATATCCGGTGGAGCATCCTGAGAAGTTTGAGAA
GTTCGGCATGTCACCTTCTAAAGGAGTTCTTTTCTATGGTCCTCCTGGTTGTGGCAAAACATTGCTGGCTAAGGCTATTG
CCAACGAATGTCAAGCTAATTTCATCAGTATCAAGGGTCCTGAGCTTCTAACCATGTGGTTTGGTGAGAGTGAAGCCAAT
GTCAGGGATGTTTTTGACAAGGCACGCCAGTCTGCTCCTTGTGTCATATTCTTCGATGAACTTGACTCCATTGCTATTCA
AAGAGGAAACAGTGTAGGAGATGCTGGTGGTGCAGCTGATAGAGTTTTGAACCAACTCCTAACTGAGATGGATGGTTTAT
CAGCCAAGAAAACCGTCTTTATAATTGGTGCTACCAACAGGCCTGATATAATCGACCCTGCACTTATGAGGCCAGGTCGC
CTTGACCAGCTAATTTATATCCCTCTGCCAGACGAAGGTTCTCGACTACAGATCTTTAAGGCTTGCTTGAGAAAATCACC
AGTCTCAAAAGATGTTGACCTTCAAGTTCTTGCCAAGCACACTGAAGGCTTTAGTGGTGCTGATATCACAGAAATCTGTC
AGAGGGCTTGCAAATATGCTGTCAGGGAGGACATCGAAAAGGATATCAAGAGGAAGATCGAGGGCCTGGAAGACAGCATG
GAAGAAGGAATGACTTGGCTTAAGGTTTCTCACTTTGAAGAGTCCATGAGGTATGCTAGGAAGAGTGTGAGTGTCTCTGA
TATTCTCAAGTACCAGATGTTTTCTCAAACTTTGCAGCAATCCAGAGGTTTTGGTTCTGATTTCAAATTTTCGGAGGCGG
CGACATCAGCTGATGGTCTTAATCCAGGTGTGACTTCAGCTGGTGGGGATGATGAACTATATTAA

Alignment

ORF - retro_ptri_3 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.98 %
• Parental protein coverage: 97.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KRDFSTAILER-KKAPNRLVVDEAVNDDNSVVSLHPETMEKLQLFRGDTILIKGKKRKDTICIALADDSC
          KRDFS..I.ER.KKAPNRL.VDEA.NDDNSV..L.P.TME.L..FRGD..LIKGKKR.DT.CIALADD.C
Retrocopy KRDFSDSIMERNKKAPNRLLVDEAINDDNSVITLNPATMEQLDIFRGDSLLIKGKKRRDTVCIALADDRC

Parental  DEPKIRMNKVVRSNLRVRLGDVVSVHQCPDVKYGKRVHILPIDDTIEGVTGNLFDAYLKPYFLEAYRPVR
          D.PKI.MNKVVRSNLRVRLGD.VSV..C....YGKRVHILP.DDT..G..G.LFDAYLKPYF....RPVR
Retrocopy DQPKILMNKVVRSNLRVRLGDMVSVQLCHNLQYGKRVHILPLDDTVDGLSGSLFDAYLKPYFKDSHRPVR

Parental  KGDLFLVRGGMRSVEFKVIETDPPEYCVVAPDTEIFCEGEPVLREDENRLDEVGYDDVGGVRKQMAQIRE
          KGDLFLVRGGMRSVEFKVIETDP.EYCVV.PDTEIFCEGE.V.REDE.RLD..GYDD.GGVRKQ.A.IRE
Retrocopy KGDLFLVRGGMRSVEFKVIETDPAEYCVVEPDTEIFCEGEAVKREDEERLDGIGYDDLGGVRKQLALIRE

Parental  LVELPLRHPQLFKSIGVKPPKGILLYGPPGSGKTLIARAVANETGAFFFCINGPEIMSKLAGESESNLRK
          .VELPLR.PQLFK.IGVKPP.GILLYGPPG.GKTLIARA.ANETGAFFFCINGPEIMSK.AGESE.NLRK
Retrocopy MVELPLRFPQLFKTIGVKPPRGILLYGPPGTGKTLIARAIANETGAFFFCINGPEIMSKMAGESEQNLRK

Parental  AFEEAEKNAPSIIFIDEIDSIAPKREKTNGEVERRIVSQLLTLMDGLKSRAHVIVMGATNRPNSIDPALR
          AFEEAEKNAP.I.FIDEIDSIAPKREKT.GEVERRIVSQLLTLMDGLK.RAHVIV.GATNRPNS.DPALR
Retrocopy AFEEAEKNAPAIVFIDEIDSIAPKREKTGGEVERRIVSQLLTLMDGLKARAHVIVIGATNRPNSLDPALR

Parental  RFGRFDREIDIGVPDEVGRLEVLRIHTKNMRLAEDVDLERIAKDTHGYVGADLAALCTEAALQCIREKMD
          RFGRFD.EIDIGVPDEVGRLEVLR.HTK.M.L.EDVDLE..AK.T.GYVGADLAALC.E.ALQCIREKM.
Retrocopy RFGRFDKEIDIGVPDEVGRLEVLRVHTKKMKLSEDVDLEKVAKGTQGYVGADLAALCSESALQCIREKMG

Parental  VIDLEDETIDAEILNSMAVTDEHFKTALGTSNPSALRETVVEVPNVSWEDIGGLETVKRELQETVQYPVE
          .IDLED.TIDAE.LNSMAVT.EHF..ALGTSNPSALRET.VEVPNV.WEDIGGLE.VK.ELQETVQYPVE
Retrocopy IIDLEDDTIDAEVLNSMAVTNEHFSIALGTSNPSALRETIVEVPNVRWEDIGGLEKVKMELQETVQYPVE

Parental  HPEKFEKFGMSPSKGVLFYGPPGCGKTLLAKAIANECQANFISIKGPELLTMWFGESEANVREIFDKARQ
          HPEKFEKFGMSPSKGVLFYGPPGCGKTLLAKAIANECQANFISIKGPELLTMWFGESEANVR..FDKARQ
Retrocopy HPEKFEKFGMSPSKGVLFYGPPGCGKTLLAKAIANECQANFISIKGPELLTMWFGESEANVRDVFDKARQ

Parental  SAPCVLFFDELDSIATQRGSSVGDAGGAADRVLNQLLTEMDGMSAKKTVFIIGATNRPDIIDPALLRPGR
          SAPCV.FFDELDSIA.QRG.SVGDAGGAADRVLNQLLTEMDG.SAKKTVFIIGATNRPDIIDPAL.RPGR
Retrocopy SAPCVIFFDELDSIAIQRGNSVGDAGGAADRVLNQLLTEMDGLSAKKTVFIIGATNRPDIIDPALMRPGR

Parental  LDQLIYIPLPDEESRFQIFKSCLRKSPVSKDVDLTALAKYTQGFSGADITEICQRACKYAIRENIEKDIE
          LDQLIYIPLPDE.SR.QIFK.CLRKSPVSKDVDL..LAK.T.GFSGADITEICQRACKYA.RE....DIE
Retrocopy LDQLIYIPLPDEGSRLQIFKACLRKSPVSKDVDLQVLAKHTEGFSGADITEICQRACKYAVRE----DIE

Parental  RERRRSENPEAMEEDVEDEVSEIKASHFEESMKYARRSVSDADIRKYQAFAQTLQQSRGFGSEFRFAEAS
          ....R....E..E...E......K.SHFEESM.YAR.SVS..DI.KYQ.F.QTLQQSRGFGS.F.F.EA.
Retrocopy KDIKRKI--EGLEDSMEEGMTWLKVSHFEESMRYARKSVSVSDILKYQMFSQTLQQSRGFGSDFKFSEAA

Parental  AGATGSDPFAASAGGADE
          ..A.G..P...SAGG.DE
Retrocopy TSADGLNPGVTSAGGDDE

Legend:

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

Expression

RNA-Seq

Populus trichocarpa was not studied using RNA-Seq expression data.

ChIP-Seq

Populus trichocarpa was not studied using ChIP-Seq data.

EST

Populus trichocarpa was not studied using EST data.

TSS

Populus trichocarpa was not studied using FANTOM5 data.

Lab

retro_ptri_3 was not experimentally validated.

Homology

Retrocopy orthology:

Populus trichocarpa 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 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Brachypodium distachyon	BRADI1G74922	1 retrocopy	retro_bdis_9,
Zea mays	GRMZM2G063060	1 retrocopy	retro_zmay_7,
Leersia perrieri	LPERR03G03650	1 retrocopy	retro_lper_1,
Hordeum vulgare	MLOC_74069	2 retrocopies	retro_hvul_38, retro_hvul_40,
Hordeum vulgare	MLOC_76416	1 retrocopy	retro_hvul_59,
Oryza glaberrima	ORGLA06G0255900	1 retrocopy	retro_ogla_73,
Populus trichocarpa	POPTR_0006s12740	1 retrocopy	retro_ptri_3 ,
Prunus persica	PRUPE_ppa001552mg	1 retrocopy	retro_pper_43,
Sorghum bicolor	Sb01g020910	1 retrocopy	retro_sbic_10,
Sorghum bicolor	Sb01g046840	1 retrocopy	retro_sbic_42,