RetrogeneDB ID: retro_xtro_30

Retrocopy location

• Organism: Xenopus (Xenopus tropicalis)
• Coordinates: GL173357.1:1063..3049(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSXETG00000033280
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: gnpat
• Ensembl ID: ENSXETG00000022535
• Aliases: None
• Description: glyceronephosphate O-acyltransferase [Source:Jamboree;Acc:XB-GENE-948374]

Sequence

>retro_xtro_30
GGAAAGTGCTTATGTGAGAGACCGTTCCGGAGCAGGAAGAGAGAGGCGTTTGAGGACATACTGGAGGCGCGGCGGCAGAC
TAGTGACCTCACCTACGCTATGAGGCGCTACACACCGGTAATTTACAGACACCTGACCCCCTGCCCGCCCAGTGCCTTAA
AGACTATGGTCCTACAGTCTGTGGAGCTGCAGTACGTCATTGGTCAGATCTCTCTGGAAATCGGGCAGCCGCTAGATTCC
CTTCAGAAACAGGCGGCGGATATTCTAGACGAAATGGGTCAGAACCTGCGGATGGAAGCCGTCCGATTCTTCGCTCTGAC
CCTCAGCAAGATCTTCAAGCGCCTCTTCCGCAAAGTGCGCGTCAACGAGGAAGGGGTCCAGCGGCTGACTCAGGCCATTC
GAGAGCACCCGGTTGTGCTGATTCCCAACCACCAAAGCTACGTCGACTTTTTGATGCTGTCCTTCGTTCTGTACACGTAC
GACCTGGCGCTTCCCGTCATCGCCGCGGGAATCGCCCTCACCGGCATGACCCTCGTAGGAGAACTGCTGCGTATGGCCGG
CGCCTTCTATATAAAGCGAGGGTTCCGAGGGAACCCACTCTATTGGGCGGTCTTTGCGGAATACGTGAAGGCCTTAGTGC
GAAGCGGTTACGCCCCGGTGGAGTTCTTCATCGAGGGCTGGAGGAGCAGAACGGGCAAGATATTAAGTCCAAAGTTTGGC
ATGTTAACTGTCGTCATGGAGCCGTTTTTTAAAGGCCAAGTGTTCGACACGTACATTGTTCCGATCAGTATTACTTATGA
ACGGGTTCTGGAAGAATCTCTTCTTGCCTATGAACTCCTAGGCGTGCCCAAACCCAAAGAGTCTACGTCGGGAATGATCA
AAGCAAGGAGTGTTCTCCATCAGAACTTTGGAAGCATCCACGTCTACTTCGGTGTGCCTTTATCATTACGTTCTCTGTCT
TATGGAAGAATAAGCCGCTCCCAGTATAATCTAACGCCCCGACACCTCCCCCAGCAACCGTCTGAAGACCTGCACCTCTT
TGTCCGCGATGTGGCTTACAAAGTGGAACTTACCCAAATCGCAAATATGGTTCTTAGCCCTGGAGTCTTGGTGGCAACCA
TTTTGCTACAGAATTTACCAGAGATGGACTTTAATGTCTTAGTTGAAAAGACTCTTTGGCTGAAAGATTTAGTAGAAGCC
TTCGGAGGGTTCCTAGAGTGGCCTGATAATGAGTCAGCCGGCGTGGTGGTCCGTTCCAGCATTGAGCTTCACTCCAACCT
TCTCCGTCTGGTCGATGGACGGGTGGCTTTGTTCGAGGAGCTCACAGGTTCAATGACGGAGGAGGTCGTCTTCAGACGAG
CAGTTTCAACCCTCACTTGTGCCTTATATAGGAACCAAGTGATCAATGTGTGTGTACGCCCTGCACTGGTGGTTCTAGCT
CGTGAAATAGTCCAGAGTTCCAGGAAAGAAGACATCTTGAATTCATTTCACTTCTTGAGGGATATCTTTTCCAAAGAGTT
CATCTTCTCCCCCAGCTCCGGAGATAAGGATTTTGAAGAAGGCTGCTCCATGTTGGCCAAATGCGACATCATTCATGTGA
CCCCTAATGAAATCAAAATAACGGACAGTGGGGCAATTGCTGCTTTGTTTTTATCGCAGATGTTCCAGCCATTTCTTGAA
GGTTACAAGTTGGCCGCTTCGTATCTGTCGAGGGAAGTTACTAATGGCTTCACGGAAATGCAATACGTGTCTGGAATGAG
GAGTTTTATTTCTCGTCTGATCGTATCCGGAGCCAGTCGGTGCGTCGAAGCTCTCTCTTCTGATATGCAAAAAAATACAC
TGTCCTCCTTTGTCCAGCTTGGGGTTATAACGAAATTGAAATCGACCAATGAGACGACCTTCTACGTAGAGAAGAGGCCA
CTGGAGGAAATGGCGGAAAAACTTGGACTGCAACTGTCCATGGAAAAAATACCGTCGGCCCGACTT

Alignment

ORF - retro_xtro_30 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.44 %
• Parental protein coverage: 99.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GSVYSQKEFRSKKREVFEDILEERRQSSDLRYAMKCYTPVIYRNLTPCTPSGLKTSVLQSLELQYVIRQI
          G.......FRS.KRE.FEDILE.RRQ.SDL.YAM..YTPVIYR.LTPC.PS.LKT.VLQS.ELQYVI.QI
Retrocopy GKCLCERPFRSRKREAFEDILEARRQTSDLTYAMRRYTPVIYRHLTPCPPSALKTMVLQSVELQYVIGQI

Parental  SSESGESCESIQEQAAEILDEMGHNLRMGAIRLFAMSLSKIFKRLFQKVCVNEEGIQRLTQAIQEHPVVL
          S.E.G....S.Q.QAA.ILDEMG.NLRM.A.R.FA..LSKIFKRLF.KV.VNEEG.QRLTQAI.EHPVVL
Retrocopy SLEIGQPLDSLQKQAADILDEMGQNLRMEAVRFFALTLSKIFKRLFRKVRVNEEGVQRLTQAIREHPVVL

Parental  LPSHRSYIDFLMMSYVLYSYDLALPVIAAGMGNDFMGMKIVGELLRMSGAFYMRRSFRGNQLYWAVFAEY
          .P.H.SY.DFLM.S.VLY.YDLALPVIAAG......GM..VGELLRM.GAFY..R.FRGN.LYWAVFAEY
Retrocopy IPNHQSYVDFLMLSFVLYTYDLALPVIAAGIA--LTGMTLVGELLRMAGAFYIKRGFRGNPLYWAVFAEY

Parental  VKTLIRNGYAPVEFFVEGQRSRTCKTLSPKFGLLNIAMEPFFKGEVFDTYIVPISINYERVLEESLYAYE
          VK.L.R.GYAPVEFF.EG.RSRT.K.LSPKFG.L...MEPFFKG.VFDTYIVPISI.YERVLEESL.AYE
Retrocopy VKALVRSGYAPVEFFIEGWRSRTGKILSPKFGMLTVVMEPFFKGQVFDTYIVPISITYERVLEESLLAYE

Parental  LLGVPKPKESTSGLIKARRILNENFGSIHIYFGQPISLRSLASGIINRTQYNLKPRHLPQRPPEDVQSFV
          LLGVPKPKESTSG.IKAR..L..NFGSIH.YFG.P.SLRSL..G.I.R.QYNL.PRHLPQ.P.ED...FV
Retrocopy LLGVPKPKESTSGMIKARSVLHQNFGSIHVYFGVPLSLRSLSYGRISRSQYNLTPRHLPQQPSEDLHLFV

Parental  RDVAYQVELNQIANMVLSPGVLVATILLQNLPGMDFNVLVEKTLWLKDLIEAFGGFLEWPDNLSASRVVR
          RDVAY.VEL.QIANMVLSPGVLVATILLQNLP.MDFNVLVEKTLWLKDL.EAFGGFLEWPDN.SA..VVR
Retrocopy RDVAYKVELTQIANMVLSPGVLVATILLQNLPEMDFNVLVEKTLWLKDLVEAFGGFLEWPDNESAGVVVR

Parental  SSIDLHSNIFTLVDGHVTLLEHKHTGLLTEEIVFEQAVSLLMCAFYRNQMINVCVRPALVVLACEMVQSS
          SSI.LHSN...LVDG.V.L.E...TG..TEE.VF..AVS.L.CA.YRNQ.INVCVRPALVVLA.E.VQSS
Retrocopy SSIELHSNLLRLVDGRVALFE-ELTGSMTEEVVFRRAVSTLTCALYRNQVINVCVRPALVVLAREIVQSS

Parental  IKEEIFRSFSFLRSVFSKEFIFFPGSEDKDFDEGCFMLTKCDIIHTTPSEIMITDKGTIAAFFLSKMFQP
          .KE.I..SF.FLR..FSKEFIF.P.S.DKDF.EGC.ML.KCDIIH.TP.EI.ITD.G.IAA.FLS.MFQP
Retrocopy RKEDILNSFHFLRDIFSKEFIFSPSSGDKDFEEGCSMLAKCDIIHVTPNEIKITDSGAIAALFLSQMFQP

Parental  FLEGYKLAYTYLVGEVTNAFTEKQYISGVRSFISRLIVSGTSKCYEALSSDMQKNILSSFVQLGVLKRMK
          FLEGYKLA..YL..EVTN.FTE.QY.SG.RSFISRLIVSG.S.C.EALSSDMQKN.LSSFVQLGV....K
Retrocopy FLEGYKLAASYLSREVTNGFTEMQYVSGMRSFISRLIVSGASRCVEALSSDMQKNTLSSFVQLGVITKLK

Parental  SVSEATFCLEKKMVKETAEKLGLQMFTEKLPSARL
          S..E.TF..EK....E.AEKLGLQ...EK.PSARL
Retrocopy STNETTFYVEKRPLEEMAEKLGLQLSMEKIPSARL

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	1.25 RPM	21.67 RPM
SRP007412_heart	0.38 RPM	22.22 RPM
SRP007412_kidney	0.38 RPM	22.22 RPM
SRP007412_liver	0.00 RPM	16.74 RPM
SRP007412_skeletal_muscle	0.25 RPM	18.74 RPM

ChIP-Seq

Xenopus tropicalis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_xtro_30 retrocopy.

TSS

Xenopus tropicalis was not studied using FANTOM5 data.

Lab

retro_xtro_30 was not experimentally validated.

Homology

Retrocopy orthology:

Xenopus tropicalis 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000012167	1 retrocopy	retro_eeur_570,
Xenopus tropicalis	ENSXETG00000022535	1 retrocopy	retro_xtro_30 ,