RetrogeneDB ID: retro_sbic_45

Retrocopy location

• Organism: Sorghum (Sorghum bicolor)
• Coordinates: GL002606.1:2606151..2607000(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Sb0012s010440
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Sb06g022840
• Aliases: None
• Description: None

Sequence

>retro_sbic_45
ATGGATCCTTGTCACCAATCCATAGAGACCGCAGGCGCGAAGGACTACAGTGACCCACCCCCAGCACCATTGGTCAACGC
CGGCGAGCTGGGCAAGTGGTCCCTCTACCGCGCCGCCATCGCCGAGTTCGTCGCCACGTTGCTCTTCGTCTACGTCACGC
TGGCCACCGTCATCGGGCACAAGCGCCAGGCCGAGTCCCAGCCGTGCGGCAGCGTCGGCGTGCTGGGCATCGCGTGGTCC
TTCGGCGGCATGATCTTCGTGCTCGTCTACTGCACCGCGGGCATCTCCGGCGGCCACATCAACCCGGCGGTCACCTTCGG
CCTTCTGCTGGCGCGCAAGGTGTCGCTTGTGCGCGCCGCGCTCTACGTGGTGGCGCAGTGCCTGGGCGCCATGTGTGGCG
CTGGCCTCGTCAAGGCCTTCCACGGGGCCCATTGGTACCTTCACTACGGCGGCGGCGCCAACGAGCTCTCCGCCGGCTAC
TCCAAGGGAGCCGGTCTGGCCGCCGAGATCGTGGGCACCTTCGTCCTCGTCTACACCGTGTTCTCGGCCACCGACCCCAA
GCGCAAGGTCAGGGATTCGCACGTCCCGGTCCTAGCGCCGCTGCCCATCGGATTCGCGGTGTTCATGGTGCACCTGGCCA
CCATCCCCGTCACCGGCACGGGCATCAACCCGGCAAGGAGCCTGGGGCCGGCCGTTGTGTACAACCAGCGAAAGGCGTGG
GAAGATCAGTGGATATTCTGGGTCGGCCCCCTCATTGGCGCTGCCGCCGCCATGATCTACCACCAGTTAGTTCTCCGCGC
CGGCGCAGCCAAGGCCTTGGCATCCTTACGCAACAACTACCATATCTGA

Alignment

ORF - retro_sbic_45 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.87 %
• Parental protein coverage: 90.41 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AKDYSDPPPAPLVDAEELTKWSLYRAVIAEFVATLLFLYITVATVIGYKHQTDASSSGPDAACGGVGILG
          AKDYSDPPPAPLV.A.EL.KWSLYRA.IAEFVATLLF.Y.T.ATVIG..H...A.S......CG.VG.LG
Retrocopy AKDYSDPPPAPLVNAGELGKWSLYRAAIAEFVATLLFVYVTLATVIG--HKRQAESQ----PCGSVGVLG

Parental  IAWAFGGMIFILVYCTAGVSGGHINPAVTFGLFLARKVSLVRALLYIVAQCLGAICGVGLVKGFQSA-FY
          IAW.FGGMIF.LVYCTAG.SGGHINPAVTFGL.LARKVSLVRA.LY.VAQCLGA.CG.GLVK.F..A..Y
Retrocopy IAWSFGGMIFVLVYCTAGISGGHINPAVTFGLLLARKVSLVRAALYVVAQCLGAMCGAGLVKAFHGAHWY

Parental  VRYGGGANGLSDGYSKGTGLAAEIIGTFVLVYTVFSATDPKRNARDSHVPVLAPLPIGFAVFMVHLATIP
          ..YGGGAN.LS.GYSKG.GLAAEI.GTFVLVYTVFSATDPKR..RDSHVPVLAPLPIGFAVFMVHLATIP
Retrocopy LHYGGGANELSAGYSKGAGLAAEIVGTFVLVYTVFSATDPKRKVRDSHVPVLAPLPIGFAVFMVHLATIP

Parental  ITGTGINPARSLGAAVIYNNDKTWDDHWIFWVGPFIGAAIAAAYHQYVLRASAAK
          .TGTGINPARSLG.AV.YN..K.W.D.WIFWVGP.IGAA.A..YHQ.VLRA.AAK
Retrocopy VTGTGINPARSLGPAVVYNQRKAWEDQWIFWVGPLIGAAAAMIYHQLVLRAGAAK

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_45 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	Sb06g022840	1 retrocopy	retro_sbic_45 ,