RetrogeneDB ID: retro_sbic_11

Retrocopy location

• Organism: Sorghum (Sorghum bicolor)
• Coordinates: 7:56519477..56521894(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Sb07g022170
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Sb02g027810
• Aliases: None
• Description: None

Sequence

>retro_sbic_11
ATGCCGCCGCCGCCGCACTACTATCCCGTCCTGCTGCCGCTACTGGTTCTTGCGGCTGTGGCGGGCGGGGGAGGGGGAGA
GGCAGATGGACTGGAGCGGACGTACATCGTGCGGGTGGACGCCGACGCGAAGCCGTCGGTGTACCCGACGCACGCGCACT
GGTACGAGGCGGCGGTGCTGGCGGCGGCCGGCGATGGCGCGGGGTGGCCGGAAGGGGGCCCGCTGATCCACACCTACTCG
GCCGCCTTCCACGGGTTCTCCGCGCGGATGTCCCCCGCGGCCGCCCAAGCGCTGGCGTCCGCGCCCGGGGTGGCGGCCGT
GGTGCCCGAGCGCGTGCGGCAGCTCGCCACCACGCGGTCCCCGAGGTTCCTCGGCTTGCTGTCCTCCCCGCCGTCGGCGC
TGCTCGCGGACTCCGACTTCGGGGCTGACCTGGTCATCGCCATCGTCGACACCGGCATCTCCCCCGCGCACCGCAGCTTC
CACGACCGCGGGCTGGGCCCGGTCCCGAGCCGGTGGCGCGGGGTGTGCGCGTCCGGGCCCGGGTTCCCGCCCAGCGCCTG
CAACCGCAAGCTCGTCGGTGCGCGGTTCTTCTCCAAGGGGTACGAGGCCACCTCGGGACGCATGAATGAGACGGCGGAGG
TCAGGTCCCCGCTCGACACCGACGGGCACGGCACCCACACCGCGTCTATCGCTGCGGGGAGGTACGTGTTCCCGGCGTCC
ACGCTTGGGTACGCGCGCGGCGTGGCCGCCGGGATGGCGCCCAAGGCGCGATTGGCAGCGTACAAGGTGTGCTGGGTGGG
TGGCTGCTTCGACTCCGACATTCTCGCGGCCTTCGACGCCGCCGTCGCCGACGGTGTCGATGTGGTTTCGCTCAGCGTCG
GTGGCGTTGTTGTGCCGTACTACCTCGACGCGATTGCTATCGGGGCGTTCGGCGCCACCGAAGCCGGTATCGTCGTCTCT
GCTTCGGCCGGCAATGGTGGTCCCGGTGGGCTCACGGTGACCAATGTGGCGCCCTGGATGGCCACCGTCGGGGCTGGCTC
CATGGACCGCGCGTTCCCGGCCAATGTGCGGCTCGGCGACGGGCAGGTGCTCGACGGCGTGAGCGTGTACGGGGGGCCAG
CGCTCGAGTCCGGCAGGATGTACGAGCTGGTGTACGCCGGGGCGAGCGGCGACGGCGGCGGCGGAGCTTCGTCCGCGTCC
GACGGGTACTCGGCGTCGATGTGCCTCGACGGCTCGCTGGACCCAGCCGCAGTGCACGGCAAGATCGTGGTGTGCGACCG
CGGCGTGAACTCGCGCGCCGCCAAGGGCGACGTGGTCCACCGCGCGGGTGGCATCGGAATGGTGCTAGCCAACGGGGCGT
TCGACGGCGAGGGCCTTGTCGCCGACTGCCACGTCCTTCCGGCGACCGCCGTCGGCGCGGCTGCGGGCGACAGGCTCCGC
AAGTACATCGCGTCGTCCACCAAGCAGAGGCCCGCCACGGGTACCATCCTGTTCGAGGGCACCCACCTGGGCGTGCACCC
GGCGCCGGTGGTGGCGGCGTTCTCGGCGCGCGGCCCGAACCCGCAATCCCCGGAGATCCTGAAGCCGGACCTGATAGCTC
CCGGCCTCAACATCCTGGCGGCGTGGCCCAGCGGCGTCGGCCCGGCCGGCATTCCCTCGGACATCCGCCGCACCGAGTTC
AACATCCTGTCAGGCACGTCCATGGCCTGCCCGCACGTGTCCGGGCTCGCCGCGCTGCTCAAGGCGGCGCACCCGACCTG
GAGCCCCGCGGCGATCAAGTCGGCGCTGATGACCACGGCCTACGTGAGGGACAACAGCAACGGGACGATGGTGGACGAGT
CGACGGGCGCGGTGGCCGGCGCGTTCGACTTCGGCGCCGGGCACGTGGACCCGATGCGCGCCATGGACCCGGGTCTGGTG
TACGACATCGGGCCGGGGGACTACGTCAACTTCCTGTGCAACCTCAACTACACGGAGCAGAACATCCGCGCCATCACGCG
GCGGCAGGCGGACTGCCGCGGCGCGCGGCGCGCCGGGCACGCGGGCAACCTCAACTACCCGTCGATGTCGGCCACGTTCG
TCGCCGCGGCGGACGGCGCCAGGGAGACGACGACGATGAGGACGCACTTCATCCGGACGGCGACCAACGTGGGCGGGGGC
GGGAAGGCGGTGTACCGCGCGTCGGTCCAGGCCCCCGAGGGGTGCAACGTGACGGTGCAGCCGCGGCAGCTGGCGTTCCG
GCGCGACGGGCAGCGGCTGAGCTTCACGGTGCGGGTGGAGGCCGCGGTGGCGGCGGCGCCCGGGAAGAGGATGGAGCCCG
GGAGCTCGCAGGTGCGGAGCGGCGCGCTGACGTGGAGCGACGGCAGGCACGTCGTCCGTAGCCCGATCGTGGTGACGGTG
CAGGCGCCATTGCAGTG

Alignment

ORF - retro_sbic_11 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.6 %
• Parental protein coverage: 59.72 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CNRKLIGARFFNKGYLATVGQQQQQQASPASTRDTDGHGTHTLSTAAGRFVRGANLFGYGNGTAKGGAPR
          CNRKL.GARFF.KGY.AT.G......A...S..DTDGHGTHT.S.AAGR.V..A...GY..G.A.G.AP.
Retrocopy CNRKLVGARFFSKGYEATSGRMNET-AEVRSPLDTDGHGTHTASIAAGRYVFPASTLGYARGVAAGMAPK

Parental  AHAAAYKVCWRPVNGSECFDADIIAAFDAAIHDGVHVLSVSLGGSPANYFRDGVAIGSFHAARHGVTVVC
          A..AAYKVCW..V.G..CFD.DI.AAFDAA..DGV.V.S.S.GG....Y..D..AIG.F.A...G..V..
Retrocopy ARLAAYKVCW--VGG--CFDSDILAAFDAAVADGVDVVSLSVGGVVVPYYLDAIAIGAFGATEAGIVVSA

Parental  SAGNSGPAAGTVSNTAPWLLTVGASTMDREFPAYLVLDNNKRIKGQSL--SPTRLAGNKY---YQLISSE
          SAGN.GP...TV.N.APW..TVGA..MDR.FPA...L.......G.S....P....G..Y...Y...S..
Retrocopy SAGNGGPGGLTVTNVAPWMATVGAGSMDRAFPANVRLGDGQVLDGVSVYGGPALESGRMYELVYAGASGD

Parental  EAKGANATVT--QAKLCIKGSLDKAKVKGKIVVCTRGNNARVEKGEAVHRAGGAGMVLANDEASGNEMIA
          ...GA........A..C..GSLD.A.V.GKIVVC.RG.N.R..KG..VHRAGG.GMVLAN....G....A
Retrocopy GGGGASSASDGYSASMCLDGSLDPAAVHGKIVVCDRGVNSRAAKGDVVHRAGGIGMVLANGAFDGEGLVA

Parental  DAHVLPATHISYTDGLELLAYLNS---RRSASGYITVPYTALDTKPAPFMAAFSSQGPNTVTPQILKPDI
          D.HVLPAT......G..L..Y..S....R.A.G.I....T.L...PAP..AAFS..GPN...P.ILKPD.
Retrocopy DCHVLPATAVGAAAGDRLRKYIASSTKQRPATGTILFEGTHLGVHPAPVVAAFSARGPNPQSPEILKPDL

Parental  TAPGVSILAAFTGQAGPTGLAFDDRRVLFNAESGTSMSCPHVAGIAGLLKALHPDWSPAAIKSAIMTTAR
          .APG..ILAA.....GP.G...D.RR..FN..SGTSM.CPHV.G.A.LLKA.HP.WSPAAIKSA.MTTA.
Retrocopy IAPGLNILAAWPSGVGPAGIPSDIRRTEFNILSGTSMACPHVSGLAALLKAAHPTWSPAAIKSALMTTAY

Parental  VQDNMRKPM-SNSSFLRATPFGYGAGHVQPNRAADPGLVYDANATDYLGFLCALGYNSSVI
          V.DN....M...S....A..F..GAGHV.P.RA.DPGLVYD....DY..FLC.L.Y....I
Retrocopy VRDNSNGTMVDESTGAVAGAFDFGAGHVDPMRAMDPGLVYDIGPGDYVNFLCNLNYTEQNI

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_11 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza barthii	OBART09G14060	1 retrocopy	retro_obar_23,
Oryza nivara	ONIVA09G14620	1 retrocopy	retro_oniv_27,
Sorghum bicolor	Sb02g027810	1 retrocopy	retro_sbic_11 ,