RetrogeneDB ID: retro_sbic_9

Retrocopy location

• Organism: Sorghum (Sorghum bicolor)
• Coordinates: 3:61507765..61508601(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Sb03g033100
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Sb04g008010
• Aliases: None
• Description: None

Sequence

>retro_sbic_9
ATGGCCGGGATCGTGGTGGTGTTCGACTTCGACAAGACGATCATCGACGTGGACAGCGACAACTGGGTGGTCGACAACCT
GGGCTTCACCGAGCTGTTCGAGCGCCTCCTCCCCACCATGCCCTGGAACACGCTCATGGACACCATGATGGGTGAGCTCC
ACGCGGCCGGCAAGACCCTGGGCGACGTCGCCGAGGTGCTGAGGGCGGCGCCCATCGACCCGCGCGTGCCCGCCGCCATC
AAGGCCGCGTACGCGCTGGGCTGCGACCTGCGCGTGCTCAGCGACGCCAACGCCTTCTTCATCGAGACCGTCCTGGAGCA
CCACGGCATCCGTGGCTGCTTCTCCCAGATCAACACCAACCCCAGCCACGTCGACGCCGACGGCCGCCTCCGCATCGGGC
CCTACCACGCCGCCCCGCACGGCTGCGGCGTCGGCACCTGCCCGCCCAACATGTGCAAGGGCCTGGTGCTCGACCGCATC
CTCCGCGAGGCGGCCGCCGGGACGACCGGGAGGTCGACGAAGCGCGTCATCTACCTCGGCGACGGCCGCGGCGACTACTG
CCCGTCGCTGCGGCTGGCCCGGGAGGACTTCATGATGCCGCGCAGGGGTTACCCCGTGTGGGACCTCATCCGCGAGGACC
CCGCGCGGGTGCAGGCGGAGGTGCACCCGTGGGCCGACGGCGCCGACCTGGAGGAGACGCTGCTGCGCCTCGTCGGGAGG
GCGCTCGTGGAGGAGGCCGCGCTGCCGCCGCCGCTCGACTGCAAGCTCGAGTCCACCATGCCCGTTGCCGCGCAGGACGG
CGGCATGCCCATCATGCCGCTCGGCGTCAAGAACTG

Alignment

ORF - retro_sbic_9 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 51.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LVVFDFDKTIVDCDSDNWVVDALGATRRFDDLLRHLPWNHAIDAMMGELHSDGKTAEDIRGSLRTAPLSP
          .VVFDFDKTI.D.DSDNWVVD.LG.T..F..LL...PWN...D.MMGELH..GKT..D....LR.AP..P
Retrocopy VVVFDFDKTIIDVDSDNWVVDNLGFTELFERLLPTMPWNTLMDTMMGELHAAGKTLGDVAEVLRAAPIDP

Parental  HVAAAIKAAYALGCELRVLSDANAFFIDTILAHHGLAAYFSGTDTNPAHVDAAGRLRIRPYHDFGAAGHG
          .V.AAIKAAYALGC.LRVLSDANAFFI.T.L.HHG....FS...TNP.HVDA.GRLRI.PYH...AA.HG
Retrocopy RVPAAIKAAYALGCDLRVLSDANAFFIETVLEHHGIRGCFSQINTNPSHVDADGRLRIGPYH---AAPHG

Parental  CTLPTCPPNMCKGKVMERILRQ
          C...TCPPNMCKG.V..RILR.
Retrocopy CGVGTCPPNMCKGLVLDRILRE

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_9 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	Sb04g008010	1 retrocopy	retro_sbic_9 ,