RetrogeneDB ID: retro_sbic_42

Retrocopy location

• Organism: Sorghum (Sorghum bicolor)
• Coordinates: 7:52266561..52268940(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Sb07g020190
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Sb01g046840
• Aliases: None
• Description: None

Sequence

>retro_sbic_42
ATGTCGAGCAGCAGCATGATGGACGCCGACGGCAAGAAAGATTTTAGCACGGCGATCCTAGAGCGCAAGAAGGCGCCGAA
CCGCCTCCTGGCGGATGACGGCGAGGGCGAGGTGGCCATCGACAACTCCATGGTGGCGCTCAGCCCCGCCACCGCGTTCC
AGCTCGAGATCTTCACCGGCGACCTCGTGCTGCTCCGCGGCAAGCGCCGCAAGGAGACCGTCTGCTACGCCGTGTTCGAC
GCCTCCTGTCCCGACGCCAGGGTGCGCCTGAACCGCGTCGTGCGCAGCAACATCCGCGTCCACCTCGGGGACATCGTCAC
CGTCAAGCGTCTCGACGAGGTCCCGACCGGCACGCGCGTCCAGATCGCGCCGTTCGAGGACACCATCACCGGCATCTCCG
GCGACCTCTTCGACGCGTACCTGAAGCCCTACTTCGGCAACGACGCGCTGCGGCCGGTGTGCAAGGGCGACCGCTTCATC
GTGCGCGGCAACATGCACGCCGTCGAGTTCAAGGTCGTCGACACGGAGCCCGCCGACCGCGTCCTCGTCCGCCCGGACAC
GGCCATCTTCTGCAGCGACCAGCCGGTCAAGCGGGAGGACGAGGAGCGGCTGGACGGCCCTGGCTACGACGACGTGGGCG
GCGTCCGCAAGCAGCTGGCCCAGATCCGCGAGCTGGTCGAGCTGCCGCTGCGCCACCCCAAGCTGTTCCAGACGCTCGGC
GTCAAGCCGCCCAAGGGGATCCTGCTCTACGGCCCGCCCGGCACCGGCAAGACGCTCCTGGCGCGCGCCATCGCGTCGGA
GTCCGGCGCCCACTTCTTGGTCGTCAACGGCCCGGAGATCATGTCCATGATGGCCGGACAGAGCGAGGCCAACCTGCGCA
ATGTTTTCGAGGACGCGGAAAAGTCGGCGCCTTCCATTATTTTCATGGACGAGATCGACGCCATCGCCCCCAACCGCGAC
AAGACGCACGGCGAGGTGGAGCGCCGCGTGGTCTCGCAGCTTCTCACGCTCATGGACGGTCTCCGGCCGCGCGCGCAGGT
CGTGGTCATCGGCGCCACCAACCGCCCCAACAGCCTGGATCCGGCGCTCCGGCGCTTTGGCCGCTTCGACAGGGAGCTTG
ACATCGGCGTGCCCGACGAGGTCGGCCGCCTCGAGATCCTCCGCATCCACAGCAAGGACATGCCGCTCGCCGAGGACGTG
GACCTCGAGCGCATCGGCAAGGACACGCACGGCTTCGTCGGCGCCGACCTCGCGGCGCTCTGCTCCGAGGCGGCCCTGCA
GTTGATCCGCGAGAAGATGGACGTGATCGACGTGGAGGAGGAGACTATCGACGTGGACGTGCTCAACTCGCTGCGCGTGT
GCAACGAGCACCTCAAGCACGCCAAGGAGGTGACCAAGCCGTCGGCGCTGCGCGAGAGAGGGCTGGTGGAGGTGCCCAAG
GTCTCGTGGGACGACATCGGCGGCCTGGAGGACGTCAAGCTGGAGCTCCAGGAGACGGTGCAGTACCCGGTGGAGCACCC
GGAGATGTTCGAGATGTTTGGCATGTCGCCGTCGCGCGGCGTGCTCTTCTACGGGCCCCCGGGCTGCGGCAAGACGATGC
TGGCCAAGGCCATCGCCAAGGAGTGCAAGGCCAACTTCATCAGCGTCAAGGGGCCCGAGCTGCTCACCATGTGGTACGGC
GAGAGCGAGTCCAACGTCCGCGACCTGTTCGACAAGGCGCGCTCGGCGGCGCCGAGCATCCTCTTCTTCGACGAGCTCGA
CTCCATCGCCGTGAAGCGCGGCAACAGCGTGGGCGACGTGGGCGGCACGTCCGACCGCGTGCTCAACCAGCTGCTCACGG
AGATGGACGGCATCAACGCGAAGAAGACGGTGTTCGTCATCGGCGCCACCAACCGCCCCGACATCATCGACCCGGCGATG
CTCCGGCCGGGGCGGCTGGACCAGCTCATCTACATCCCGCTGCCCGACGAGCCCTCGCGGCTGCAGATCTTCAAGTCGTG
CCTGCGGCGGTCCCCCGTCTCCCGCCGCGTCCACCTGCCGGCGCTGGCGCGCCTCACGGCCGGGTTCAGCGGCGCCGACA
TCGCGGAGATCTGCCAGCGCGCGTGCAAGCTGGCGGTGCGCGACGTGATCCAGCGGAGCCTCAAGGTGGGCAAGGCCGCG
GCCATGCGCGGTGCGGAGATGGGAATAGGGCACTTCACGGAAGCCCTGAAGCATGCCAGGCGGAGCGTCAGCGACCTGGA
CGTGATGAAGTACGACTTCTTGGCGAAGCGGCTCAAGGGCGGGGCTGGCTTCGAGGACGAGCCCATCATTGCTGCCCCGA
TGGGGAAGGAGCCGCTGATCACAGAGATGGAAGACGACGACGACAGCTTGCTGTACTAA

Alignment

ORF - retro_sbic_42 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.59 %
• Parental protein coverage: 87.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SSSDPKGKKDYSTAILERKKSPNRLVVDEATND---DNSVVALHPDTMERLQLFRGDTVLLKGKKRKDTI
          S..D..GKKD.STAILERKK.PNRL..D........DNS.VAL.P.T...L..F.GD.VLL.GK.RK.T.
Retrocopy SMMDADGKKDFSTAILERKKAPNRLLADDGEGEVAIDNSMVALSPATAFQLEIFTGDLVLLRGKRRKETV

Parental  CIVLADDTCEEPKVRMNKVVRKNLRVRLGDVVSVHQCPDVKYGKRVHILPIDDTIEGITGNLFDAFLKPY
          C....D..C....VR.N.VVR.N.RV.LGD.V.V.....V..G.RV.I.P..DTI.GI.G.LFDA.LKPY
Retrocopy CYAVFDASCPDARVRLNRVVRSNIRVHLGDIVTVKRLDEVPTGTRVQIAPFEDTITGISGDLFDAYLKPY

Parental  F-LEAYRPLRKGDLFLVRGGMRSVEFKVIETDPIEYCIVAPDTEIFCEGEPVKREDEERLDEVGYDDVGG
          F...A.RP..KGD.F.VRG.M..VEFKV..T.P.....V.PDT.IFC...PVKREDEERLD..GYDDVGG
Retrocopy FGNDALRPVCKGDRFIVRGNMHAVEFKVVDTEPADRVLVRPDTAIFCSDQPVKREDEERLDGPGYDDVGG

Parental  VRKQMAQIRELVELPLRHPQLFKSIGVKPPKGILLFGPPGSGKTLIARAVANETGAFFFLINGPEIMSKL
          VRKQ.AQIRELVELPLRHP.LF...GVKPPKGILL.GPPG.GKTL.ARA.A.E.GA.F...NGPEIMS..
Retrocopy VRKQLAQIRELVELPLRHPKLFQTLGVKPPKGILLYGPPGTGKTLLARAIASESGAHFLVVNGPEIMSMM

Parental  AGESESNLRKAFEEAEKNAPSIIFIDEIDSIAPKREKTHGEVERRIVSQLLTLMDGLKSRAHVIVMGATN
          AG.SE.NLR..FE.AEK.APSIIF.DEID.IAP.R.KTHGEVERR.VSQLLTLMDGL..RA.V.V.GATN
Retrocopy AGQSEANLRNVFEDAEKSAPSIIFMDEIDAIAPNRDKTHGEVERRVVSQLLTLMDGLRPRAQVVVIGATN

Parental  RPNSIDPALRRFGRFDREIDIGVPDEVGRLEVLRIHTKNMKLAENVDLELIAKDTHGYVGADLAALCTEA
          RPNS.DPALRRFGRFDRE.DIGVPDEVGRLE.LRIH.K.M.LAE.VDLE.I.KDTHG.VGADLAALC.EA
Retrocopy RPNSLDPALRRFGRFDRELDIGVPDEVGRLEILRIHSKDMPLAEDVDLERIGKDTHGFVGADLAALCSEA

Parental  ALQCIREKMDIIDLEDETIDAEILNSMAVTNDHFKTALGTSNPSALRET-VVEVPNVSWEDIGGLENVKR
          ALQ.IREKMD.ID.E.ETID...LNS..V.N.H.K.A.....PSALRE...VEVP.VSW.DIGGLE.VK.
Retrocopy ALQLIREKMDVIDVEEETIDVDVLNSLRVCNEHLKHAKEVTKPSALRERGLVEVPKVSWDDIGGLEDVKL

Parental  ELQETVQYPVEHPEKFEKFGMSPSKGVLFYGPPGCGKTLLAKAIANECQANFISVKGPELLTMWFGESEA
          ELQETVQYPVEHPE.FE.FGMSPS.GVLFYGPPGCGKT.LAKAIA.EC.ANFISVKGPELLTMW.GESE.
Retrocopy ELQETVQYPVEHPEMFEMFGMSPSRGVLFYGPPGCGKTMLAKAIAKECKANFISVKGPELLTMWYGESES

Parental  NVREIFDKARQSAPCVLFFDELDSIATQRGSSVGDAGGAADRVLNQLLTEMDGMNAKKTVFIIGATNRPD
          NVR..FDKAR..AP..LFFDELDSIA..RG.SVGD.GG..DRVLNQLLTEMDG.NAKKTVF.IGATNRPD
Retrocopy NVRDLFDKARSAAPSILFFDELDSIAVKRGNSVGDVGGTSDRVLNQLLTEMDGINAKKTVFVIGATNRPD

Parental  IIDPALLRPGRLDQLIYIPLPDEQSRLQIFKACLRKSPVAKDVDLNALAKYTQGFSGADITEICQRACKY
          IIDPA.LRPGRLDQLIYIPLPDE.SRLQIFK.CLR.SPV...V.L.ALA..T.GFSGADI.EICQRACK.
Retrocopy IIDPAMLRPGRLDQLIYIPLPDEPSRLQIFKSCLRRSPVSRRVHLPALARLTAGFSGADIAEICQRACKL

Parental  AIRENIEKDIE
          A.R..I.....
Retrocopy AVRDVIQRSLK

Legend:

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

Expression

RNA-Seq

Sorghum bicolor was not studied using RNA-Seq expression data.

ChIP-Seq

Sorghum bicolor was not studied using ChIP-Seq data.

EST

Sorghum bicolor was not studied using EST data.

TSS

Sorghum bicolor was not studied using FANTOM5 data.

Lab

retro_sbic_42 was not experimentally validated.

Homology

Retrocopy orthology:

Sorghum bicolor 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Zea mays	GRMZM2G063060	1 retrocopy	retro_zmay_7,
Leersia perrieri	LPERR03G03650	1 retrocopy	retro_lper_1,
Oryza glaberrima	ORGLA06G0255900	1 retrocopy	retro_ogla_73,
Populus trichocarpa	POPTR_0006s12740	1 retrocopy	retro_ptri_3,
Sorghum bicolor	Sb01g020910	1 retrocopy	retro_sbic_10,
Sorghum bicolor	Sb01g046840	1 retrocopy	retro_sbic_42 ,