RetrogeneDB ID: retro_sbic_10

Retrocopy location

• Organism: Sorghum (Sorghum bicolor)
• Coordinates: 1:70510070..70512412(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Sb01g047410
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Sb01g020910
• Aliases: None
• Description: None

Sequence

>retro_sbic_10
ATGAAGAAGGCGGCGAACAAGCTGGTGGTGGAGGAGCCGACCAACGACGACGTCTCCATATGCAACCTCCACCCGGCGAC
CATGGAGAAGCTGTCCATCTACCACGGCGACGTGGTCCTGCTCAAGGGGAAGCGGCGCCGCGACACGATCTGCATCGCCA
TGAACAACGAGGGGTGCGGGGAGCACGCGCTCGGCATCAACCGGTCCGTCCGCTCCAACCTCCGGGTGCGCCTGGGCGAC
GTCGTGTCCGTGCACCCGTGCCACGACGCCGCGTACGGGGCCAAAGTGCATGTCCTGCCCCTCGACGACACCGTGGAGGG
CCTCACGGGGGACCTCTTCGAGGCCTACCTGAAGCCGCACTTCCTCAACGCCTACCGCCCCGTCCGCAAGGGCGACCTCT
TCCTCGTGCGCGGCGGCATGAGGAGTGTGGAATTCAAGGTGGTGGACATCCACCCGCCCGCCGAGTACTGCATCGTCGCC
GACGACACGGTGGTGTTCTGCGATGGCGAGCCCGTGAAGCGGGAAGACGAGGAGAGGCTCGATGGCGTTGGCTACGATGA
CGTTGGTGGCATGCGGAAGCAGCTGGCTCAGATCAGGGAGCTGGTCGAGCTCCCACTCAGGCACCCGCAGTTGTTCAAGT
CGATTGGAGTGAAGCCCCCCAAGGGCATCCTATTGTACGGGCCGCCTGGCTCCGGAAAGACTCTCATTGCCCGTGCAGTC
GCTAACGAAACCGGCGCCTTCTTCTTCTGCATAAACGGTCCCGAGATCATGTCGAAGCTAGCCGGAGAGAGCGAGAGCAA
TCTTCGAAAAGCATTCCAGGAGGCGGAGAAGAACGCGCCGTCCATCATCTTTATTGATGAAATCGACTCTATCGCGCCCA
AGAGGGAGAAGACACACGGCGAGGTGGAGAGGCGCATTGTGTCCCAGCTTCTCACGCTCATGGACGGCCTCAAGACACGC
GCGCATGTCATTGTCATGGGCGCGACGAACCGCCCCAACAGCATCGACCCCGCCCTGCGACGCTTCGGCCGGTTCGATCG
CGAGATTGACATCGGCGTGCCGGACGAGGTCGGACGCCTCGAGGTGCTGCGCGTGCACACCAAGAATATGAAGCTCGCCG
AGGACGTCAACCTGGAGGCCGTGTCCAAGGACACGCACGGGTATGTCGGCGCCGACCTGGCCGCGCTCTGCACCGAGGCC
GCGCTGCAGTGTATCAGGGAGAAGATGGACGTCATTGACCTCGAGGACGACACGATCGACGCGGAGATCCTCAACTCGAT
GGCCATCACGAACGACCACCTCAAGACCGCCCTCGCCGGCACCAACCCGTCGGCGCTACGCGAGACCGTTGTGGAGGTGC
CTAACGTCAGCTGGGCGGACATCGGAGGCCTGGAGGGCGTCAAGCGGGAGCTGCAGGAGACCGTGCAGTACCCCGTGGAG
CACCCGGACATGTTCGAGAAGTTCGGCATGTCTCCGTCCAGGGGCGTGCTCTTCTACGGGCCGCCTGGGTGCGGCAAGAC
GCTGCTCGCCAAGGCGATCGCGAACGAGTGCCAGGCCAACTTCATCAGCGTCAAGGGTCCGGAGCTGCTGACCATGTGGT
TCGGCGAGAGCGAGGCCAACGTCCGAGACATCTTCGACAAGGCGCGGCAGTCGGCGCCGTGCGTCCTCTTCTTCGACGAA
CTGGACTCGATCGCCATGCAGAGGGGCAGCCACGTGGGCGACGCCGGCGGCGCGGCGGACAGGGTCCTGAACCAGCTCCT
CACCGAGATGGACGGCATGAGCGCCAAGAAGACGGTGTTCATCATCGGCGCCACAAACCGGCCGGACATCATCGACCCGG
CGCTGCTTCGGCCTGGTCGCCTGGACCAGCTGATCTACATCCCGTTGCCAGACGAGGCCTCGCGGCAACAGATCTTCAAG
GCCTGCCTCAGGAAGTCCCCCGTGGCCAAGAACGTCGACCTCGGTGCGCTGGCCAGGTTCACGGCAGGGTTCAGCGGCGC
GGACATCACGGAGATTTGCCAGAGGGCGTGCAAGTACGCCATCAGAGAGGACATCGAGAAGGACATCGAGAGGGAGAGGA
AGGCCAAGGAGAATCCGGGGGAAATGGCGGTGGACTGCGCCGACGACGAGCCGGCGCAGATCGGGGCCGTGCATTTCGAG
GAGTCCATGAGGTACGCGCGGAGGAGCGTCAGCGACGCGGACATCCGAAAGTACCAGGCGTTCGCGCAGACGCTGCAGCA
GTCGAGGGGATTCGGCACCGAGTTCCGCTTCCCCATCCGGCCCCAACAGGCGGCAGAAGCAGAGGCGGCGGCCGACTCTG
AGGAGGATGATATTTACAGCTG

Alignment

ORF - retro_sbic_10 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.95 %
• Parental protein coverage: 94.69 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KKSPNRLVVDEATNDDNSVVALHPDTMERLQLFRGDTVLLKGKKRKDTICIVLADETCEEPKVRMNKVVR
          KK..N.LVV.E.TNDD.S...LHP.TME.L....GD.VLLKGK.R.DTICI....E.C.E.....N..VR
Retrocopy KKAANKLVVEEPTNDDVSICNLHPATMEKLSIYHGDVVLLKGKRRRDTICIAMNNEGCGEHALGINRSVR

Parental  QNLRVRLGDVVSVHQCQDVKYGKRVHILPIDDTVEGITGNLFDAFLKPYFLEAYRPLRKGDLFLVRGGMR
          .NLRVRLGDVVSVH.C.D..YG..VH.LP.DDTVEG.TG.LF.A.LKP.FL.AYRP.RKGDLFLVRGGMR
Retrocopy SNLRVRLGDVVSVHPCHDAAYGAKVHVLPLDDTVEGLTGDLFEAYLKPHFLNAYRPVRKGDLFLVRGGMR

Parental  SVEFKVIETDP-AEYCIVAPDTEIFCDGEPIKREDEERLDEVGYDDVGGVRKQMAQIRELVELPLRHPQL
          SVEFKV....P.AEYCIVA.DT..FCDGEP.KREDEERLD.VGYDDVGG.RKQ.AQIRELVELPLRHPQL
Retrocopy SVEFKVVDIHPPAEYCIVADDTVVFCDGEPVKREDEERLDGVGYDDVGGMRKQLAQIRELVELPLRHPQL

Parental  FKSIGVKPPKGILLYGPPGSGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPS
          FKSIGVKPPKGILLYGPPGSGKTLIARAVANETGAFFF.INGPEIMSKLAGESESNLRKAF.EAEKNAPS
Retrocopy FKSIGVKPPKGILLYGPPGSGKTLIARAVANETGAFFFCINGPEIMSKLAGESESNLRKAFQEAEKNAPS

Parental  IIFIDEIDSIAPKREKTNGEVERRIVSQLLTLMDGLKSRSHVIVMGATNRPNSIDPALRRFGRFDREIDI
          IIFIDEIDSIAPKREKT.GEVERRIVSQLLTLMDGLK.R.HVIVMGATNRPNSIDPALRRFGRFDREIDI
Retrocopy IIFIDEIDSIAPKREKTHGEVERRIVSQLLTLMDGLKTRAHVIVMGATNRPNSIDPALRRFGRFDREIDI

Parental  GVPDEVGRLEVLRIHTKNMKLAEDVNLELISKDTHGYVGADLAALCTEAALQCIREKMDIIDLEDETIDA
          GVPDEVGRLEVLR.HTKNMKLAEDVNLE..SKDTHGYVGADLAALCTEAALQCIREKMD.IDLED.TIDA
Retrocopy GVPDEVGRLEVLRVHTKNMKLAEDVNLEAVSKDTHGYVGADLAALCTEAALQCIREKMDVIDLEDDTIDA

Parental  EILNSMAVTNDHFKTALGTSNPSALRETVVEVPNVSWEDIGGLENVKRELQETVQYPVEHPEKFEKFGMS
          EILNSMA.TNDH.KTAL...NPSALRETVVEVPNVSW.DIGGLE.VKRELQETVQYPVEHP..FEKFGMS
Retrocopy EILNSMAITNDHLKTALAGTNPSALRETVVEVPNVSWADIGGLEGVKRELQETVQYPVEHPDMFEKFGMS

Parental  PSKGVLFYGPPGCGKTLLAKAIANECQANFISVKGPELLTMWFGESEANVREIFDKARQSAPCVLFFDEL
          PS.GVLFYGPPGCGKTLLAKAIANECQANFISVKGPELLTMWFGESEANVR.IFDKARQSAPCVLFFDEL
Retrocopy PSRGVLFYGPPGCGKTLLAKAIANECQANFISVKGPELLTMWFGESEANVRDIFDKARQSAPCVLFFDEL

Parental  DSIATQRGSSVGDAGGAADRVLNQLLTEMDGMNAKKTVFIIGATNRPDIIDPALLRPGRLDQLIYIPLPD
          DSIA.QRGS.VGDAGGAADRVLNQLLTEMDGM.AKKTVFIIGATNRPDIIDPALLRPGRLDQLIYIPLPD
Retrocopy DSIAMQRGSHVGDAGGAADRVLNQLLTEMDGMSAKKTVFIIGATNRPDIIDPALLRPGRLDQLIYIPLPD

Parental  EQSRLQIFKACLRKSPVAKDVDLNALAKYTQGFSGADITEICQRACKYAIRENIEKDIERERRRKDNPEA
          E.SR.QIFKACLRKSPVAK.VDL.ALA..T.GFSGADITEICQRACKYAIRE.IEKDIERER..K.NP..
Retrocopy EASRQQIFKACLRKSPVAKNVDLGALARFTAGFSGADITEICQRACKYAIREDIEKDIERERKAKENPGE

Parental  MEED-EVDEIAEIKAAHFEESMKYARRSVSDADIRKYQAFAQTLQQSRGFGSEFRF--SEQSATAGAAAA
          M..D...DE.A.I.A.HFEESM.YARRSVSDADIRKYQAFAQTLQQSRGFG.EFRF....Q.A....AAA
Retrocopy MAVDCADDEPAQIGAVHFEESMRYARRSVSDADIRKYQAFAQTLQQSRGFGTEFRFPIRPQQAAEAEAAA

Parental  D
          D
Retrocopy D

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_10 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Brachypodium distachyon	BRADI1G74922	1 retrocopy	retro_bdis_9,
Hordeum vulgare	MLOC_74069	2 retrocopies	retro_hvul_38, retro_hvul_40,
Hordeum vulgare	MLOC_76416	1 retrocopy	retro_hvul_59,
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,