RetrogeneDB ID: retro_sbic_17

Retrocopy location

• Organism: Sorghum (Sorghum bicolor)
• Coordinates: 10:17959912..17961003(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Sb10g012150
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Sb04g029750
• Aliases: None
• Description: None

Sequence

>retro_sbic_17
ATGGCGGAGCGGCGGAGCAATGGCGGCTTCGCGTCCCAAAGCAGCCATTTGGCGGCGATGATGAGAGGAAGCTACGCGCC
CCAGAGCCTCTGGCGCCCGTCGTCGACGTCGATGCCGATGCCGGTCGGTGGTGCAGCGGTTGTGGCCTCGGCGCCCGCCG
AGAAGAACAAGAAGAGCTTCGCCGCCGACTTCCTGCTGGGCGGGGTGTCGTCGTCGGTGTCCAAGACGGTGGCGGCGCCG
ATCGAGCGCGTGAAGATGCTGCTGCAGAACCAGGACGAGCTGATCCGCACCGGCAGGCTGTCGGAGCCGTACAGGGGCAT
CGGCGACTGCTTCGGCCGCACCGTCCGGGACGAGGGCGTCCTGTCGCTGTGGCGCGGCAACACCACCAACGTCATCCGCT
ACTTCCCCACGCAGGCGCTCAACTTCGCGTTCAAGGACTACTTCAAGTCCCTCTTCAACTTCAACCGGGACAGGGACGGG
TACTGGCGGTGGTTCGCCGGGAACATCGTCTCGGGGAGCGCCGCCGGGGCCACGTCGCTGCTCTTCGTCTACTCCCTCGA
CTACGCCAGGACGCGTCTCACCAACGACTACAAGGCGGCGGCGGCCATGGGCAAGGGCGGCGAGAGGCAGTTCACGGGGC
TCGTCGACGTCTACCGGAAGACGCTCCGGTCCGATGGCGTCGCCGGGCTGTACCGAGGGTTCAACGTCTCGGTGGTCGGG
ATCGTCGTCTACCGGGGCCTCTACTTCGGCATGTACGACTCCTTCAAGCCGGTGCTGCTCACGGGGAAGCTGCAGGACAA
CTTCTTCGCGAGCTTGGCGCTCGGCTGGATGATCACCAATGGCGCCAACCTCGCCTCGTACCCGCTCGACACTGTCCGGA
GAAGGATGATGATGACCTCGGGGGAGGCCGTCAAGTACAAGAGCTCCATGGACGCCTTCGCCCAGATCGTCAGGAACGAG
GGACCCAGGTCGCTCTTCAAAGGCGCCGGCGCCAACGTCCTACGCGCCATCGCCGGCGCTGGCGCGCTTGCCGGCTACGA
CCAGCTGCAGCTCATCTTCTTCGGCAAGAAGTACGGCTCAGGTGGCGCCTA

Alignment

ORF - retro_sbic_17 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.24 %
• Parental protein coverage: 90.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SVSSYERSFATRNYMTQSLFSPSMSVTGGINVPVMRTPLFANAPAEKGGKNFMIDFMMGGVSAAVSKTAA
          S.SS.........Y..QSL..PS.........PV......A.APAEK..K.F..DF..GGVS..VSKT.A
Retrocopy SQSSHLAAMMRGSYAPQSLWRPSST---SMPMPVGGAAVVASAPAEKNKKSFAADFLLGGVSSSVSKTVA

Parental  APIERVKLLIQNQDEMIKSGRLSEPYKGIGDCFKRTIKDEGFSSLWRGNTANVIRYFPTQALNFAFKDYF
          APIERVK.L.QNQDE.I..GRLSEPY.GIGDCF.RT..DEG..SLWRGNT.NVIRYFPTQALNFAFKDYF
Retrocopy APIERVKMLLQNQDELIRTGRLSEPYRGIGDCFGRTVRDEGVLSLWRGNTTNVIRYFPTQALNFAFKDYF

Parental  KRLFNFKKDKDGYWKWFAGNLASGGAAGASSLFFVYSLDYARTRLANDAKAAKG---GGDRQFNGLVDVY
          K.LFNF..D.DGYW.WFAGN..SG.AAGA.SL.FVYSLDYARTRL.ND.KAA.....GG.RQF.GLVDVY
Retrocopy KSLFNFNRDRDGYWRWFAGNIVSGSAAGATSLLFVYSLDYARTRLTNDYKAAAAMGKGGERQFTGLVDVY

Parental  RKTLKSDGIAGLYRGFNISCVGIIVYRGLYFGLYDSIKPVVLTGNLQDNFFASFALGWLITNGAGLASYP
          RKTL.SDG.AGLYRGFN.S.VGI.VYRGLYFG.YDS.KPV.LTG.LQDNFFAS.ALGW.ITNGA.LASYP
Retrocopy RKTLRSDGVAGLYRGFNVSVVGIVVYRGLYFGMYDSFKPVLLTGKLQDNFFASLALGWMITNGANLASYP

Parental  IDTVRRRMMMTSGEAVKYKSSLDAFQQILKKEGPKSLFKGAGANILRAIAGAGVLSGYDQLQILFFGKKY
          .DTVRRRMMMTSGEAVKYKSS.DAF.QI...EGP.SLFKGAGAN.LRAIAGAG.L.GYDQLQ..FFGKKY
Retrocopy LDTVRRRMMMTSGEAVKYKSSMDAFAQIVRNEGPRSLFKGAGANVLRAIAGAGALAGYDQLQLIFFGKKY

Parental  GSGGA
          GSGGA
Retrocopy GSGGA

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_17 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Sorghum bicolor	Sb04g029750	1 retrocopy	retro_sbic_17 ,
Setaria italica	Si017474m.g	1 retrocopy	retro_sita_52,