RetrogeneDB ID: retro_sbic_15

Retrocopy location

• Organism: Sorghum (Sorghum bicolor)
• Coordinates: 4:67912993..67914235(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Sb04g038550
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Sb02g042320
• Aliases: None
• Description: None

Sequence

>retro_sbic_15
ATGATGAACTGCTTGCGCCTGCGTCTCTGCTACCACCGCGACGTGGATCCGTCGTCCCCCTGCGGCAGCCCCTCCAGCTA
CGCGGCCCAGACCCAGAGCTCCGTCCACGTACGCGGCGGCGGCGGCGGCGGCACCACGACCACCCGCAAGTTCACGCTGG
CGCAGCTGTCCGTGGCCACGGGCGGGTTCCCTGAGTCGAACCTGGTGGGCGAGGGCGGGTTCGGCAGGGTGTACAGGGGC
CGGCTGGATGCGGCCGGTGGCGGTGGCCTCGAGGTGGCCGTGAAGCAGCTTTGCCGCGGCGGCGCGCAGGGCAGCCGCGA
GTTCCTGGTGGAGTGCAGCATGCTGATGATGCTGCGGCACCCGAACCTGGTGTCCCTGGTGGGCTACTGCGCCGAGGCCC
AGGAGCGGCTCCTCGTCTACGAGTTGCTCCCGCGGGGCAGCCTGGACGCGCACCTCTTCGTCTCCAAGTCCCTGCTTGGC
TGGGACGCCCGCGTGAAGGTCGCCCTTGGCGCCGCCCGCGGCCTCCGCTACCTCCACGAGGTGGTGACCCCGCCGGTGAT
CTACCGCGACCTCAAGTCGTCCAACATCCTGCTGGGCGACGACCTGAGCCCCAAGCTGTCGGACTTTGGGCTCGCCAGGC
TGGGCCCCGACCCCGAGGGCGACGACACCCACGTGTCCACCCGCGTCATGGGCACCTACGGCTACTGTGCCCCGGAGTAC
GCCGTCACTGGGAAGCTCAGCGTCAAGTCCGACGTCTACAGCTTCGGCGTCGTGCTGCTGGAGCTGCTCACGGGGCGAAG
GGCCTTCGACTTGGACGCCCACAGCAGCAGCAGCAGTAGTAGTAGTAGTAGGGATGATCAGGAGGCTCATCAGGACCAGG
AGCGGCGGCTGCTGGTGTGGGCACGGCCCCACCTGCAGCAGCTGCAGGGGCGGGGCAGGGGCAGGGGCCTGGAGGCGCTG
GCGGACCCGGCGTTGCAGGGGCGGTACCCTCGCCGCGGACTCTACCAGGTGGCCGTCATCGCCTCGCTCTGCCTGCACGA
CAAGCCCAACCTCCGCCCCACTATGACCGACGTCACGCAGGCGCTGGAGCACGTGGCGGCGCAGCCCTGGAGGGTTGTTG
TTAGTAGGGATAGAGACGGCGATATGATCAGGAGGAGGCCGGCTGCCGGCGGCGGATCATCAAGACGGGGACGGGGACGG
GGAAGCACTCCGCGCGCCTCCTCCGCTGACAGTGACAGCTAG

Alignment

ORF - retro_sbic_15 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.07 %
• Parental protein coverage: 51.74 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SKKEDSVPVRRGGNIPHGPAQIFTFRELAIATKNFRKDCLLGEGGFGRVYKGRME----NGQVIAVKQLD
          .....SV.VR.GG.........FT...L..AT..F....L.GEGGFGRVY.GR.......G...AVKQL.
Retrocopy AQTQSSVHVRGGGGGGTTTTRKFTLAQLSVATGGFPESNLVGEGGFGRVYRGRLDAAGGGGLEVAVKQLC

Parental  RNGFQGNREFLVEVLMLSLLHHPNLVRLIGYCADGDQRLLVYEYMLLGSLENHLFGPPDKEPLDWNTRMK
          R.G.QG.REFLVE..ML..L.HPNLV.L.GYCA....RLLVYE....GSL..HLF....K..L.W..R.K
Retrocopy RGGAQGSREFLVECSMLMMLRHPNLVSLVGYCAEAQERLLVYELLPRGSLDAHLF--VSKSLLGWDARVK

Parental  IAAGAAKGLEYLHDKANPPVIYRDFKSSNILLGEDYYPKLSDFGLAKLGP--VGDKTHVSTRVMGTYGYC
          .A.GAA.GL.YLH....PPVIYRD.KSSNILLG.D..PKLSDFGLA.LGP...GD.THVSTRVMGTYGYC
Retrocopy VALGAARGLRYLHEVVTPPVIYRDLKSSNILLGDDLSPKLSDFGLARLGPDPEGDDTHVSTRVMGTYGYC

Parental  APEYAMTGQLTLKSDVYSFGVVFLELITGRKAID
          APEYA.TG.L..KSDVYSFGVV.LEL.TGR.A.D
Retrocopy APEYAVTGKLSVKSDVYSFGVVLLELLTGRRAFD

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_15 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	Sb02g042320	1 retrocopy	retro_sbic_15 ,