RetrogeneDB ID: retro_sbic_47

Retrocopy location

• Organism: Sorghum (Sorghum bicolor)
• Coordinates: 2:71482609..71483065(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Sb02g037080
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Sb07g001620
• Aliases: None
• Description: None

Sequence

>retro_sbic_47
ATGGGCCGCATGTACGGGCCCGGGAAGGGCATGTCCTCGTCGGTGCTGCCCTACGCTCGCGCCGCCCCTGGCTGGGTGAG
GTCGACCGCCGCGGACGTGGAGGAGATGATCGTGCGCGCCGCCAAGAAGGGCCACCTGCCGTCGCAGATCGGTGCGCTTC
TCCGCGACACGCACGGCGTCCCGCTGGTCCACGGCGTCACGGGCGGCAAGATCCTGCGCATGCTCAAGGCCCGCGGCCTC
GCGCCGGAGGTGCCCGAGGACCTCTACTTCCTCATCAAGAAGGCCGTCGCGATCAGGAAGCACCTGGACAGGAACCGCAC
GGACGTGGACGCCAAGTTCCGCCTCATCCTCGTCGAGAGCAGGGTCCACCGCCTGATCCGCTACTACCGCCGCACCAAGA
AGATCGCCCCCAACTTGAAGTACGAATCCACCACCGCGAGCGCTCTTGTGGCGTGA

Alignment

ORF - retro_sbic_47 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.17 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGRMHSRGKGISSSALPYKRTPPTWLKTAASDVEEMITKAAKKGQMPSQIGVLLRDQHGIPLVKSVTGSK
          MGRM...GKG.SSS.LPY.R..P.W....A.DVEEMI..AAKKG..PSQIG.LLRD.HG.PLV..VTG.K
Retrocopy MGRMYGPGKGMSSSVLPYARAAPGWVRSTAADVEEMIVRAAKKGHLPSQIGALLRDTHGVPLVHGVTGGK

Parental  ILRILKAHGLAPEIPEDLYFLIKKAVAIRKHLERNRKDKDSKFRLILVESRIHRLARYYKRTKKLPPTWK
          ILR.LKA.GLAPE.PEDLYFLIKKAVAIRKHL.RNR.D.D.KFRLILVESR.HRL.RYY.RTKK..P..K
Retrocopy ILRMLKARGLAPEVPEDLYFLIKKAVAIRKHLDRNRTDVDAKFRLILVESRVHRLIRYYRRTKKIAPNLK

Parental  YESTTASTLVA
          YESTTAS.LVA
Retrocopy YESTTASALVA

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_47 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA027748	1 retrocopy	retro_oind_48,
Leersia perrieri	LPERR08G01520	1 retrocopy	retro_lper_15,
Oryza brachyantha	OB02G23100	1 retrocopy	retro_obra_7,
Oryza punctata	OPUNC08G01190	1 retrocopy	retro_opun_35,
Oryza glaberrima	ORGLA08G0005800	1 retrocopy	retro_ogla_42,
Oryza sativa japonica	OS08G0117300	1 retrocopy	retro_osat_33,
Sorghum bicolor	Sb07g001620	1 retrocopy	retro_sbic_47 ,