RetrogeneDB ID: retro_sbic_52

Retrocopy location

• Organism: Sorghum (Sorghum bicolor)
• Coordinates: 3:4930121..4930391(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Sb05g001215
• Aliases: None
• Description: None

Sequence

>retro_sbic_52
TCAGATATTGGACATTACAGTATAGTTAATCTGTTCTTGAATTCTGAATGTGCAGGGCTGCGGAGGAGCGGCAAGAGCTG
CAGGCTGCGGTGGATGAACTACCTGCGCCCGGACCTCAAGAAGGAGCCCATCTCCAAGCGCGAGGAGGAGACCATCATCT
CCTTGCAGCAGTCGCTTGGCAACCGGTGGTCGACGATCGCGGCGAGGATGCCGGGCAGGACGGACAACGAGATCAAGAAC
TACTGGAACTCACGCATCAGGAAGCGCCTC

Alignment

ORF - retro_sbic_52 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.22 %
• Parental protein coverage: 58.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SHITHYGVGTWSSVAELAGLKRSGKSCRLRWMNYLQPDLSREPISKQEEDLIVSLQKLLGNRWSAIAARM
          S.I.HY.........E.AGL.RSGKSCRLRWMNYL.PDL..EPISK.EE..I.SLQ..LGNRWS.IAARM
Retrocopy SDIGHYSIVNLFLNSECAGLRRSGKSCRLRWMNYLRPDLKKEPISKREEETIISLQQSLGNRWSTIAARM

Parental  PGRTDNEIKNYWNSRIKKKL
          PGRTDNEIKNYWNSRI.K.L
Retrocopy PGRTDNEIKNYWNSRIRKRL

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_52 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	Sb05g001215	1 retrocopy	retro_sbic_52 ,