RetrogeneDB ID: retro_sbic_46

Retrocopy location

• Organism: Sorghum (Sorghum bicolor)
• Coordinates: 3:6721497..6722567(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Sb03g006570
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Sb03g028430
• Aliases: None
• Description: None

Sequence

>retro_sbic_46
ATGGCGACGCCCTGCAATGAGCTGGAGCACAAGGCGAGGGAGGCCTTCGTGGACGACGACTTCGCACTCGCCGCCGCGCT
CTACACGCAGGCCATCGCAGCGGGCCCGCCGACCGCCGCGCTCTACGCCGACCGCGCCCAGGCCTACACCAAGATTGGCG
ACTTCGCGGCGGCTGCCGCGGACGCCGCCCGCGCCGTCGAGCTCGACCCCGCCATGGCCCGGGCGCACCTCCGCAGAGCC
CACGCCTGCGTCAAGCTGGAGCAGTACGACGCCGCCAGGGCCGCCGTCGAGGCCGGCGCCGCCCTGTCCCCCGGCGACGC
GCGGTTCGCCAGGCTGATGAAAGAGATCGACGGCAAGGCGCCCAAGCCGATGGAGACCGACGCGAGCCCCGCTGTCGCCG
TCGCCACCGCCGCGCCCGTGCCCGTGCCTGCTCCCGCTGAGAAGCCCAAGTACAGGCACGACTTCTACAACAGCGCGGCG
GAGGTGGTGGTGACCGTGTTCGCCAAGGGCGTGGCGCCGGAGCACGTCGCGGTGGAGTTCGGCGAGCAGATGCTGAGCGT
CTCCGTCGAGGTCCCCGGCGAGGCGGCGTACCACCTGCAGCCCCGCCTGTTCGGCAAGATCGTCCCCGACAAGTGCAGGT
TCGCCGTGCTCTCTACCAAGATCGAGGTCCGCCTCGCCAAGGCGGAGCCGGGGACGACGTGGACGTCGCTGGAGTTCACC
GACAAGCCCAAGTTCACCGCCGCGGCGTCACCGGTGGCGAGCGGCGGCGGCGGCGCCCAGAGGCCGTGCTACCCGTCGTC
GTCGTCCAGGGGCAGGAAGAAGGATTGGGACAAGGTCGAGGCGCAGGTGAAGAAGGAAGAGAAGGAGGAGAAGCTGGACG
GCGACGCGGCGGCCAACAGGTTCTTCCAGGACATCTTCGGCAACGCCGACGAGGACATGCGGCGGGCGATGATGAAATCG
TTCCAGGAGTCCAATGGCACTGTGCTGTCCACCGACTGGAAGGACGTCGGCTCCAAGAAGATCGAGCCCAGCCCGCCGGA
AGGCATGCATCTGCGCAAGTGGGAGTATTG

Alignment

ORF - retro_sbic_46 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.13 %
• Parental protein coverage: 57.69 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PVVEPPSKPKYRHDYYNSATEVVLTIFAKGVPADSVVIDFGEQMLSVSIEVPGEEPYHFQPRLFAKIIPE
          PV..P..KPKYRHD.YNSA.EVV.T.FAKGV....V...FGEQMLSVS.EVPGE..YH.QPRLF.KI.P.
Retrocopy PVPAPAEKPKYRHDFYNSAAEVVVTVFAKGVAPEHVAVEFGEQMLSVSVEVPGEAAYHLQPRLFGKIVPD

Parental  KCKYQVLSTKVEIRLAKAEQ-VTWTTLDYSGRPK--AVPQKISTPAETAPRPSYPSSKA---KKDWDKLE
          KC...VLSTK.E.RLAKAE...TWT.L.....PK..A...........A.RP.YPSS.....KKDWDK.E
Retrocopy KCRFAVLSTKIEVRLAKAEPGTTWTSLEFTDKPKFTAAASPVASGGGGAQRPCYPSSSSRGRKKDWDKVE

Parental  AEVKKEEKEEKLDGDAALNKFFRDIYKDADEDMRRAMMKSFVESNGTVLSTNWKDVGSKKVEGSPPDGME
          A.VKKEEKEEKLDGDAA.N.FF.DI...ADEDMRRAMMKSF.ESNGTVLST.WKDVGSKK.E.SPP.GM.
Retrocopy AQVKKEEKEEKLDGDAAANRFFQDIFGNADEDMRRAMMKSFQESNGTVLSTDWKDVGSKKIEPSPPEGMH

Parental  LKKWEY
          L.KWEY
Retrocopy LRKWEY

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_46 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	Sb03g028430	1 retrocopy	retro_sbic_46 ,
Setaria italica	Si001973m.g	1 retrocopy	retro_sita_24,