RetrogeneDB ID: retro_sbic_6

Retrocopy location

• Organism: Sorghum (Sorghum bicolor)
• Coordinates: 7:53640961..53641924(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Sb07g020760
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Sb02g024090
• Aliases: None
• Description: None

Sequence

>retro_sbic_6
ATGGCGAGCCTGACGGTGCCGCCGGTGCCGACGTGGCCACGGCAGGACGCGATCGACCTCCACAAGGCGTTCCGCGGGTT
CGGCTGCGACAGCACGACGGTGATCAGCATCCTGGCGCACCGCGACGCGGCGCAGCGCGCGGCGATCGCCCAGGAGTACC
GCGCCGTGTTCAACCAGGACCTCGCCCGCCGTCTCGCGTCGGAGCTCAGCGGCAACCACAAGCGCGCCATGCTGCTGTGG
GTCCTGGACCCGGCGACGCGCGACGCCACCGTCCTGAAGCAGGCCCTGACGGGCGACGTCACCGACCTGCGCGCCGCCAC
GGAGGTGGTCTGCTCGCGGACGCCGTCGCAGCTGGCGGTGGTGCGGCACGCGTACCGCGCCAGGTTCGGCTGCCACCTCG
AGCACGACGTGACGGAGCGGACCTCCGGCGACCACCAGCGGCTCCTGCTCGCGTACCTGGCCGTCCCGCGCGCCGAGGGC
GGCGCGGTGGTGGTGGACGCGTCGACGGTGGCGCTGGACGCGCGCGACCTCTACAAGGCCGGCGAGCGGCGGCTGGGCAC
GGACGAGCGCGCCTTCATCCGCGTCTTCAGCGAGCGGAGCTGGCCGCACATGGCGGCGGTGGCGCGCGCGTACCACCACA
TGTACGACCGGTCCCTGGAGAGCGCCGTCAAGAGCGAGACGTCGGGTAACTTCGGCTTCGGCCTCCTCACCGTGCTCCGG
TGCGCCGACAGCCCCGCCAGGTACTTCGCCGGGGTGCTGCACAAGGCCATGAAAGGGCTGGGCACCTCGGACTCGACGCT
CATCAGGGTCGTCGTCACCAGGGCCGAGATCGACATGCAGTACATCAAGGCGGAGTATCACCGGATGTACAAGCGCTCGC
TCGCCGACGCCATCCACGCCGAGACGTCCGGCAACTACCGAACCTTCCTCCTCTCCCTCGTCGGCCGCGACCGAACCTAC
TGA

Alignment

ORF - retro_sbic_6 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.52 %
• Parental protein coverage: 99.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASLTLPPAPPNPRQDAIDLHKAFKGFGCDSTAVINILTHRDSVQRGLIQQEYRAMYHEELFHRISSELS
          MASLT.PP.P..PRQDAIDLHKAF.GFGCDST.VI.IL.HRD..QR..I.QEYRA.....L..R..SELS
Retrocopy MASLTVPPVPTWPRQDAIDLHKAFRGFGCDSTTVISILAHRDAAQRAAIAQEYRAVFNQDLARRLASELS

Parental  GNHKKAMSLWILDPAGRDATVLREALSGDTMDLRAATEIICSRTPSQLQIMKQTYYARFGTYLEHDIGHH
          GNHK.AM.LW.LDPA.RDATVL..AL.GD..DLRAATE..CSRTPSQL......Y.ARFG..LEHD....
Retrocopy GNHKRAMLLWVLDPATRDATVLKQALTGDVTDLRAATEVVCSRTPSQLAVVRHAYRARFGCHLEHDVTER

Parental  TSGDHQKLLLAYVGIPRYEGPE--VDPTIVTHDAKDLYKAGEKRLGTDEKTFIRVFTERSWAHLASVSSA
          TSGDHQ.LLLAY...PR.EG....VD...V..DA.DLYKAGE.RLGTDE..FIRVF.ERSW.H.A.V..A
Retrocopy TSGDHQRLLLAYLAVPRAEGGAVVVDASTVALDARDLYKAGERRLGTDERAFIRVFSERSWPHMAAVARA

Parental  YHHMYDRKLEKVVKSETSGNFEFALLTILRCAENPAKYFAKLLRKAMKGLGTDEKTLTRVVVTRTEIDMQ
          YHHMYDR.LE..VKSETSGNF.F.LLT.LRCA..PA.YFA..L.KAMKGLGT...TL.RVVVTR.EIDMQ
Retrocopy YHHMYDRSLESAVKSETSGNFGFGLLTVLRCADSPARYFAGVLHKAMKGLGTSDSTLIRVVVTRAEIDMQ

Parental  YIKAEYFKKYKKPLAEAINSETSGNYRAFLLSLVG
          YIKAEY...YK..LA.AI..ETSGNYR.FLLSLVG
Retrocopy YIKAEYHRMYKRSLADAIHAETSGNYRTFLLSLVG

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_6 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
Zea mays	GRMZM2G009136	1 retrocopy	retro_zmay_25,
Sorghum bicolor	Sb02g024090	1 retrocopy	retro_sbic_6 ,
Setaria italica	Si030120m.g	1 retrocopy	retro_sita_33,