RetrogeneDB ID: retro_sbic_25

Retrocopy location

• Organism: Sorghum (Sorghum bicolor)
• Coordinates: 9:58106832..58108389(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Sb09g029460
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Sb03g026950
• Aliases: None
• Description: None

Sequence

>retro_sbic_25
ATGGACAGCGACAGCGAAGAAGGCGACTTCTCCACGTACGCGCAAGTGGAACGGGCCTTCAACTCCATGGAGGGCCCGTC
CGCGCAGGAGCGCATCGACTGCATCGTCCCCTTCCTCGTGTCCCTCCTGCCCGCGCCCTACGTCCCGGCCCTCGAGGTCG
AGCCCGACTCCGACGATGACCGCTTCTCGCTCACCTCCTCCGACTCCGAGTCCGGGGCGTCCGACGACCACGACGCGCTC
GCGTTCGCGGCCGTGCCGGGCGATGGCGAGGACCGCATCAGCCGCCTCCCGGACACGCTCCTGGCCGACATCATCCACCG
CCTCCCCACCAAGGACGCCGGGCGCACCGCCACGCTCTCCACGCACTGGCGCCGCATGTGGGCCGGGACCCCGCTCCTTG
TCGACGACGCGCACCTCCTCGGCGCCGGAGGGACCAACGACGTCCCCGTCGTGCGCGCGCTCGCGCGCTGCGTGGCCGCG
CACCCGGGCCCCGTCCGCGGCGCGCGCGTCACCCGCGTCTCCTTCCACGCTCACGAGTACGCGCTCCGGCGCTTGGTCGC
GGACCTCGCCGACAAGGACGTCCGGGACCTCATCCTCGTCAACCGCCCGTGGCCGCTCGACATGCCGCTCCCCGACGACA
TCCTCCGCTGCGCCTCCCTCGAACGCCTCTACCTCGGCGTATGGAAATTCCCCAAGACGACAGCCGCGCACCCGCCTGTG
TTCCCCGACCTCCGTGAGCTCGGACTCTTCCACAGCCTCGTCCGCAACGAAGAACTCGACTCCCTGCTCGCGCACTGCCC
CAAGCTGGAGGTCCTCTCTCTCGTCATGTCGTACCACGAGCCGTTGCGTCTCCACCTAACCTCCAACAGCCTCAAGATCG
CGGTGGAATGGATGTCGTCCTTCGACGAGGTCGTTGTTGAAGACGCCCCAAGCCTCGAGCGGCTGCTCTTCCAGAGCATC
TTGGGGAGGAAGCCCGTCAAGATTTTTCGTGCGCCGAGGCTGGAGGTGCTTGGGGTCCTCGACCTCGACCTCCACAAGCT
TGAGATCGGTGGCACTGTCATCAAGGCTGGGTTGAAAGTGAGTGCTAGCAACATGGTACCAAGCTTAAAGATACTAGCCG
TGAAGGTTCAGTTTGAATGCAACAGGGAGGCCAAGATGTTGTCTACTTTGCTGAAATGCTTTCCTTGCTTGGAGACGCTT
CACATAATGCCCACTCCATCTGAGACACCAGACAGCATACATGAACATGACTTGAGGTTCTGGGAGCACTTGGGTCCTTG
TGAATGCCTTGAGTCGCACCTGAAGACTGTTATGCTCCATGGGTCCTTGGTGGAAGGTCATGGGGCTGGTTTTGTCAGGT
ATGTCATGAGGGAGGGCAAGACACTCAAGACTATCGCCATTGTTTGCAGTGATGAGGAGGCGAGCGGCTGTAGAGAGTCA
GCTGTTGGCCGAAGCGGTGAAATTACTCTTTGTATTGCCACCCCACGCTGGTGTTTCCAAGCTGCCATTGATTTGTCACT
GGACGATCCCTTTGGTTCGGTGAGGCCTCAGGCATGA

Alignment

ORF - retro_sbic_25 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.92 %
• Parental protein coverage: 78.31 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VPAPEVAGDDSDSDSEHERFSLTSSDSSEASGGVGADPAAAFHPAAVGDGEDHISHLPDALLSNIISRLT
          .PAP.V.......DS...RFSLTSSDS.....G...D..A....A..GDGED.IS.LPD.LL..II.RL.
Retrocopy LPAPYVPALEVEPDSDDDRFSLTSSDSES---GASDDHDALAFAAVPGDGEDRISRLPDTLLADIIHRLP

Parental  TKEAARTAVLSTRWGGVWAATPLLVDDAHFFGADRHSDIPIMRAVSRCVAAHPGPVRAVRVTRVSFHANE
          TK.A.RTA.LST.W...WA.TPLLVDDAH..GA....D.P..RA..RCVAAHPGPVR..RVTRVSFHA.E
Retrocopy TKDAGRTATLSTHWRRMWAGTPLLVDDAHLLGAGGTNDVPVVRALARCVAAHPGPVRGARVTRVSFHAHE

Parental  YPLQRLVADLADKDVKDLILFNRPWPLNMPLPVDILRCASLERLYLGVWHFPEITAARPSVFHELRELGL
          Y.L.RLVADLADKDV.DLIL.NRPWPL.MPLP.DILRCASLERLYLGVW.FP..TAA.P.VF..LRELGL
Retrocopy YALRRLVADLADKDVRDLILVNRPWPLDMPLPDDILRCASLERLYLGVWKFPKTTAAHPPVFPDLRELGL

Parental  FHCVVRDKDLDTLLAHCPKLEIFSIVMSYGAPSRLRIVSPSLRVAVDWQSTLREVSVEDAPCLERMIFHT
          FH..VR...LD.LLAHCPKLE..S.VMSY..P.RL...S.SL..AV.W.S...EV.VEDAP.LER..F..
Retrocopy FHSLVRNEELDSLLAHCPKLEVLSLVMSYHEPLRLHLTSNSLKIAVEWMSSFDEVVVEDAPSLERLLFQS

Parental  IETRRSIKIVSAPRLQVLGFLNLNLHKLEIGGTAIRAGMNVGARAMVPSLKILAVTLQFACNQEAKMLPT
          I..R...KI..APRL.VLG.L.L.LHKLEIGGT.I.AG..V.A..MVPSLKILAV..QF.CN.EAKML.T
Retrocopy ILGRKPVKIFRAPRLEVLGVLDLDLHKLEIGGTVIKAGLKVSASNMVPSLKILAVKVQFECNREAKMLST

Parental  LLKCFPHLEKLHVLAIPSKPPSS--AHGLEFWESLDSCECLRLRLNTLNVYGCLVQTNEIGFLQYMIREG
          LLKCFP.LE.LH....PS..P.S...H.L.FWE.L..CECL...L.T....G.LV.....GF..Y..REG
Retrocopy LLKCFPCLETLHIMPTPSETPDSIHEHDLRFWEHLGPCECLESHLKTVMLHGSLVEGHGAGFVRYVMREG

Parental  KALRAVGL
          K.L.....
Retrocopy KTLKTIAI

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_25 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Sorghum bicolor	Sb03g026950	1 retrocopy	retro_sbic_25 ,