RetrogeneDB ID: retro_sbic_43

Retrocopy location

• Organism: Sorghum (Sorghum bicolor)
• Coordinates: 9:3589037..3590804(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Sb09g003220
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Sb01g050330
• Aliases: None
• Description: None

Sequence

>retro_sbic_43
ATGTTGGAGGAGCTGCTCATCTTCACGCGCGGCGGCCTGATCCTATGGGCGCTCAGCGGCGGCGGCGGCGGCAAGGGCTC
GCCGGTGGACGCGCTCATCCGCAACTGCCTCCTCGAGGAGCGGTCCGCCGGCGGCGACGGGCCGGGCTTCTTCCAGGACG
GCAAGCACGCGCTCAAGTGGGCGTTCCACAACGGGCTCGGCCTCGTCTTCGTGGCGGTGTACCGGCGCGTGCTCCGCCTC
CTCTACGTCGACGACCTCCTCGCCGCCGTCCGCGCCGAGTTCGCGCGGGTCTATCACCCCAAGCGCACCACCTACGACGG
CTTCGGCGACGTGTTCCGGCAGCTCCACCTCGAGGCCCAAGCGCGCGCCGAGGAGATGAGCAGGGCGAATAATAAACAGA
AGCCCGTTGATGCTGCGTCGCCCCATCGCCGTCCGCGGCCACAACCACCTGTCGTCCACAATTCTCCTGGTGATTCTGAA
TCTGACGGCAATGGTGGCAATGGTGATGGGAGCAAGAAGGATTCCTCCGATGGCGTCTCCGGGGAGAAAGAGGAGGAGAA
GGAAGATGGCCAGGCCTTTGATCTGAGTTTCTTCTCGAATCTGCGAACAAGGTTCACCCACAGAAATAAGGATAAGACTA
ACACCAACAAGCCGATCAAGAAAGATGTTAATAAGAGGAAAAACCCTAGGGATGGGAACAACAATGAGCATTCAGACAGG
AAGCTGGATTTCTCAGACCCAACTGATGCCAGCAAGCAGACGGATAATGCGCGAGTCAATCAGGGACAGAGCAAGGTCGA
TCTTGCTGAAACGGTTGAAGATGGCACAAGAACCAAAGGATGGTTCTCCTCAGTGTTCCAGAGCATCGCAGGTGGCAACA
GCGTAATCGAAAGGTCCGATCTGCAACCAGCGCTCAAGGCTCTCAAAGACAGGCTGATGACCAAGAACGTGGCGGAGGAG
ATCGCCGAGAAGCTCTGCGAGTCCGTGGCGGCAAGCCTGGAGGGCAAGAAGCAGGGGTCTTTCACGAGCACAGCCTCCAC
CGTCCAGGCAGCCATGGAGGCGGCTCTCGTGCGCATCCTGACGCCAAGCCGGTCCATCGACGTGCTGAGAGACGTGCACG
CGGCCAAGGACAGTGGGAGGCCGTACGTCATCGTCTTCGTCGGGGTGAACGGCGTCGGCAAGTCCACCAACCTCGCCAAG
GTCGCCTACTGGCTCCTCCAGCACGACCTCACCGTCACCCTCGCGGCGTGCGACACCTTCCGGTCCGGCGCCGTCGAGCA
GCTGCGCACCCACGCGCGCAGGCTCCAGATACCCGTCTTCGAGAAAGGGTACCAGAGAGACCCGGCGGTCGTGGCGAAGC
AGGCCATAGAGGAAGCGGCGCGGAGCAGGTCAGACGTCGTCCTGGTCGACACCGCTGGGCGTATGCAGGACAACGAGCCG
CTCATGAGGGCGCTCTCCAAGCTCATCGCCGTCAACAGCCCGGACCTCGTCCTGTTCGTCGGAGAGGCGTTGGTTGGGAA
CGACGCCGTCGATCAGCTCACCCAGTTCCACCAGAAGCTCGCGGACCTGTCGCCTGTTCATGTAGAGAAGAGGTTGATCG
ATGGCATCCTGCTCAGCAAGTTTGACACGGTTGATGACAAGGTTGGTGCGGCGCTCTCCATGGTTTATGTGTCTGGAGCT
CCGGTCATGTTTGTTGGCTGTGGTCAGTCTTACACTGACCTCAAGAAGCTGAATGTTAAGTCCATTGTTAACACCCTGCT
CAAGTGA

Alignment

ORF - retro_sbic_43 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.89 %
• Parental protein coverage: 50.8 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EEVEDGPKKKGWFSSMFQSIAG-NNVLEKSDLQPALKALKDRLMAKNVAEEIAEKLCESVAASLEGKKLG
          E.VEDG...KGWFSS.FQSIAG.N.V.E.SDLQPALKALKDRLM.KNVAEEIAEKLCESVAASLEGKK.G
Retrocopy ETVEDGTRTKGWFSSVFQSIAGGNSVIERSDLQPALKALKDRLMTKNVAEEIAEKLCESVAASLEGKKQG

Parental  SFTRISSTVQTAMEDALLRILTPRRSIDILRDVHAAKERGRPYVIVFVGVNGVGKSTNLAKVAYWLLQHN
          SFT...STVQ.AME.AL.RILTP.RSID.LRDVHAAK..GRPYVIVFVGVNGVGKSTNLAKVAYWLLQH.
Retrocopy SFTSTASTVQAAMEAALVRILTPSRSIDVLRDVHAAKDSGRPYVIVFVGVNGVGKSTNLAKVAYWLLQHD

Parental  LSVTLAACDTFRSGAVEQLRTHARRLQIPIFEKGYEKDPAVVAREAIQEATRNKSDVVLVDTAGRMQDNE
          L.VTLAACDTFRSGAVEQLRTHARRLQIP.FEKGY..DPAVVA..AI.EA.R..SDVVLVDTAGRMQDNE
Retrocopy LTVTLAACDTFRSGAVEQLRTHARRLQIPVFEKGYQRDPAVVAKQAIEEAARSRSDVVLVDTAGRMQDNE

Parental  PLMRALSKLINLNSPDLVLFVGEALVGNDAVDQLTKFNQKLADLSAVPT-ARLIDGILLTKFDTIDDKVG
          PLMRALSKLI..NSPDLVLFVGEALVGNDAVDQLT.F.QKLADLS.V....RLIDGILL.KFDT.DDKVG
Retrocopy PLMRALSKLIAVNSPDLVLFVGEALVGNDAVDQLTQFHQKLADLSPVHVEKRLIDGILLSKFDTVDDKVG

Parental  AALSMVYISGAPVMFVGCGQSYTDLKKLNVKSIVKTLLK
          AALSMVY.SGAPVMFVGCGQSYTDLKKLNVKSIV.TLLK
Retrocopy AALSMVYVSGAPVMFVGCGQSYTDLKKLNVKSIVNTLLK

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_43 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Brachypodium distachyon	BRADI1G78220	1 retrocopy	retro_bdis_6,
Sorghum bicolor	Sb01g050330	1 retrocopy	retro_sbic_43 ,
Setaria italica	Si034718m.g	1 retrocopy	retro_sita_46,