RetrogeneDB ID: retro_sbic_13

Retrocopy location

• Organism: Sorghum (Sorghum bicolor)
• Coordinates: 2:417566..418643(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Sb02g000460
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Sb06g022880
• Aliases: None
• Description: None

Sequence

>retro_sbic_13
ATGGAGGACTACGACTACGAGCCGCCGTTGATGGCCACGTACAGGCATCTCTTGGACAGTCACCCGCACCGACTGGACGT
CGTCGATCATCGGAGCGGCGCCGACGACGACGAGGAGGGCTTCCTCCTCCCGGTGATCGACCTTTCCAGCCTGCTGGAGC
AGTCATCATCAGGCGCCGAGGCAGCAGCAGAGCAGTGCCGGGCGTCCATCGTGCGCGCCGCCTCGGAGTGGGGCTTCTTC
CAGGTGACCAACCACGGCGTGCCGCAGGCGCTGCTGGACGAGCTGCACCAGGCGCAGGTCGCCGTCTTCCGCCGGCCCTT
CCACCTCAAGGCGAGCCAGCCGCTGCTGGACTTCTCGCCGGAGAGCTACCGCTGGGGCACACCCACCGCAACGTGCCTCG
ACCAACTCTCGTGGTCCGAGGCCTACCACATCCCCACGACCAATACGACGGCGGCGGCTGACGACAAGACCAGGCTCGTG
GTGGAGGAGGTGTCCACGGCGATGTCGAAGCTGGCGCAGCGGCTGGCAGGGATCCTCGTCGCAGACCTGCTGCTGGGCGA
CAGTAGCATCGGCGACGGCGAGGACGACGACACGGCAGCGGCGGTGGTGTCGCGGTGCACGCGGAGCACCTGCTTCCTAA
GGCTGAACCGGTACCCGCCGTGCCCGGCGCCCAGCGGCGCCTACGGGCTGTGCCCGCACACGGACAGCGACTTCCTCACC
ATCCTGCACCAGGACGGCGTCGGCGGCCTCCAGCTCGTCAAGGCCGGGCGGTGGGTCGCCGTCAAGCCCAACCCCGGCGC
GCTCATCGTCAACGTGGGCGACCTCCTGCAGGCGTGGAGCAACGACCGGTACCGGAGCGTCGAGCACCGGGTCATGGCCA
GCGACGCGCGGGAGCGGTTCTCCGTCGCCTTCTTCCTCTGCCCCAGCTACGACACGCTCGTCCGGCCACGCTGCGGCGCC
GGCGGACCTCCTCGCTACGAGAGCTTCACCTTCGGGGAGTACCGGAACCAGATCAGGGAGGACGTCAGGCTCACGGGCCG
AAAGCTCGGCCTGCAACGCTTTCGCAAACCAGAGTAA

Alignment

ORF - retro_sbic_13 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.04 %
• Parental protein coverage: 86.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LPLIDLSCLQQRSGGGGGSARAACADAMARAASEWGFFQVTGHGVSRALLERLRAEQARLFRLPFETKAK
          LP.IDLS.L...S..G...A...C.....RAASEWGFFQVT.HGV..ALL..L...Q...FR.PF..KA.
Retrocopy LPVIDLSSLLEQSSSGAEAAAEQCRASIVRAASEWGFFQVTNHGVPQALLDELHQAQVAVFRRPFHLKAS

Parental  AGLLN---GSYRWGAPTAATSLRHLSWSEAFHVPLASISGAACDFGDLSSLRGVMQEVADAMSRVAKTVA
          ..LL.....SYRWG.PTA.T.L..LSWSEA.H.P......AA.D.......R.V..EV..AMS..A...A
Retrocopy QPLLDFSPESYRWGTPTA-TCLDQLSWSEAYHIPTTNTT-AAAD----DKTRLVVEEVSTAMSKLAQRLA

Parental  VALAGSLLQG----GGHDEHEAAAAFPAGCDETTCYLRLNRYPACPFAADTFGLVPHTDSDFLTVLCQDH
          ..L...LL.G....G.......AAA....C...TC.LRLNRYP.CP......GL.PHTDSDFLT.L.QD.
Retrocopy GILVADLLLGDSSIGDGEDDDTAAAVVSRCTRSTCFLRLNRYPPCPAPSGAYGLCPHTDSDFLTILHQDG

Parental  VGGLQLLKDGRWVAVKPRPDALIVNIGDLFQAWSNNRYKSVEHKVVANATAERFSAAYFLCPSYDS---P
          VGGLQL.K.GRWVAVKP.P.ALIVN.GDL.QAWSN.RY.SVEH.V.A....ERFS.A.FLCPSYD....P
Retrocopy VGGLQLVKAGRWVAVKPNPGALIVNVGDLLQAWSNDRYRSVEHRVMASDARERFSVAFFLCPSYDTLVRP

Parental  VGTCGEPSPYRDFTFGEYRRKVQEDVKRTGRKIGLPNFLKQQ
          ....G.P..Y..FTFGEYR....EDV..TGRK.GL..F.K..
Retrocopy RCGAGGPPRYESFTFGEYRNQIREDVRLTGRKLGLQRFRKPE

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_13 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
Zea mays	GRMZM2G006964	1 retrocopy	retro_zmay_24,
Sorghum bicolor	Sb06g022880	1 retrocopy	retro_sbic_13 ,
Setaria italica	Si012266m.g	1 retrocopy	retro_sita_32,