RetrogeneDB ID: retro_sbic_58

Retrocopy location

• Organism: Sorghum (Sorghum bicolor)
• Coordinates: 7:57099712..57100318(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Sb01g034640
• Aliases: None
• Description: None

Sequence

>retro_sbic_58
TCCAGGGCGGCGTGGGCGGCATCCACCACGGTGGCCATAGGTGCCAGTTGCGGCAGGTCTATATCCATTAGGCTGACCCC
GTCGCCGCATTGTCCTCTGGCGGAAGGAAGAGGAAGGGCTAGCGGCGGGGCGAGGCCAAGCCCCCGAGCCCGCCACCGCC
GCCACAGCCCCTGCCTCGACAGAGCGAGACCCCGAGCAGCAAGAAGTCTGGCGCGAGGCCGTCGGGCGAGGCCAAGAAGA
GCCGCCGCCCAGTGGAGCTGGGAGAAGCGCGCGGCCCGCAGAGGCTGGAGGGCGGCGAGGTGAGGAGGGGAATATTATAT
GCAGCAGCAGCAGCAAGAGAAGGCGAAGGCGAAGAGGCTGGTGCGGTGGAAGTGCGCGAGCGGATGCAGCGCATGTTGCA
AGCTGTTCAAGGGCCCCGACTTCCCCACTCGTGACGAGATCTTTGCCGACCATCCCGATGGCCTCAAGCTGTACAGGATC
GGCTCTGATGGATGGTGCATCAACTACGACAAGGCCACCCGCACCTGCAACATCTACCAAGACCGACCTAGATTCTGCAG
GGTGGAACCAAAGGTTTTTGATGAGTTCTTTGGCGTGCCACGCAAC

Alignment

ORF - retro_sbic_58 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.99 %
• Parental protein coverage: 78.46 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ARAAWAASTAVAAGASGGRSISIRLIP-VAALSSGGRKRKGQRRGEAKPPSPPPP-QPLPRQSETLSSKK
          .RAAWAAST.VA.GAS.GRSISIRL.P.VAALSSGGRKRKG.RRGEAKPPSPPPP.QPLPRQSET.SSKK
Retrocopy SRAAWAASTTVAIGASCGRSISIRLTP<VAALSSGGRKRKG*RRGEAKPPSPPPPPQPLPRQSETPSSKK

Parental  KSGAKPSGEAKKSRRPVELGEARGPRRLEGSEARKGNV-QQQQQQEKAKAKRLVRWKCASGCGACCKLDK
          .SGA.PSGEAKKSRRPVELGEARGP.RLEG.E.R.G....QQQQQEKAKAKRLVRWKCASGC.ACCKL.K
Retrocopy -SGARPSGEAKKSRRPVELGEARGPQRLEGGEVRRGIL>MQQQQQEKAKAKRLVRWKCASGCSACCKLFK

Parental  GPDFPTPDEIFADHPDDLQLYRSMIGSDGWCVNYDKATRTCNIYQDRPSFCRVEPKVFDEFFGVPRS
          GPDFPT.DEIFADHPD.L.LYR..IGSDGWC.NYDKATRTCNIYQDRP.FCRVEPKVFDEFFGVPR.
Retrocopy GPDFPTRDEIFADHPDGLKLYR--IGSDGWCINYDKATRTCNIYQDRPRFCRVEPKVFDEFFGVPRN

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_58 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	Sb01g034640	1 retrocopy	retro_sbic_58 ,