RetrogeneDB ID: retro_sbic_31

Retrocopy location

• Organism: Sorghum (Sorghum bicolor)
• Coordinates: 7:129320..130027(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Sb07g000300
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Sb06g033470
• Aliases: None
• Description: None

Sequence

>retro_sbic_31
ATGACAAGCGAGTCCGCCACCGTGATCCAGATGGACGACGGCAGGGCCCCGGCACCAGCAGCAGCAGGAGCAGCCGCCGC
CGCCGCCGCGTCGTCGTCCTACGCCACTGCTCCAACAAGTATCAGTGCTGCTGAACCAGCGGCGGCGCCGCGCAAGACGA
CCACCGTCCCGTTCCTGCTGCGCTCGGGCGCCGAGGGGTTCCGGCGCTGTCTGGCCGTGATCGACTTCCTTCTAAGGGTA
GCCGCCTTCGGGCCCACGCTGGCGGCCGCCATCTCCACGGGCACCGCCGACGAGAGGCTGTCCGTGTTCACCAACTTCTT
CCAGTTCCATGCGAGGTTCGACGACTTCCCGGCCTTCACCTTCTTCCTGGTGGCCAACGCCGTCGCCGCGGGGTACCTGG
TGCTGTCGCTGCCCTTCTCCGTCGTGGTCATCCTCCGGCCCAACAAGGCCACGGGCGGCGTCAGGCTGCTCCTGCTCCTC
TGCGACGTGCTGATCATGGCGCTGCTCACGGCGGCCGGCGCCGCCGCCGCGGCCATCGTGTACGTGGCGCACTCGGGCAA
CCGGCGCGCCAACTGGGTTCCCATCTGCATGCAGTTCCATGGATTCTGCCAGCGCACCAGCGGCTCCGTCGTCGCCACCT
TCCTCGCCGTGCTCGTCTTCATCGTGCTCATCCTCATGGCCGCCTGCGTCATCAGACGCAGCAAGTG

Alignment

ORF - retro_sbic_31 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.88 %
• Parental protein coverage: 89.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GKAPAVATAPPPPAAAAAVPAAATTTAPRKTG-VPFFRR--ADRGSRCVALLDFVLRVAAFGPALAAAIA
          G.A.A.A.......A.....AA....APRKT..VPF..R..A....RC.A..DF.LRVAAFGP.LAAAI.
Retrocopy GAAAAAAASSSYATAPTSISAAEPAAAPRKTTTVPFLLRSGAEGFRRCLAVIDFLLRVAAFGPTLAAAIS

Parental  TGTSDETLSVFTQFFQFHARFDDFPALLFFMVANAIAAGYLVLSLPFSAVIVLRPQAI--GLRHLLLVCD
          TGT.DE.LSVFT.FFQFHARFDDFPA..FF.VANA.AAGYLVLSLPFS.V..LRP.....G.R.LLL.CD
Retrocopy TGTADERLSVFTNFFQFHARFDDFPAFTFFLVANAVAAGYLVLSLPFSVVVILRPNKATGGVRLLLLLCD

Parental  MIIAALLTAAAAAAAAIVDLAHSGNLRANWVPICMQFHGFCQRTSGAVVGSFLAVLVLLFLVILAAFAIR
          ..I.ALLTAA.AAAAAIV..AHSGN.RANWVPICMQFHGFCQRTSG.VV..FLAVLV...L...AA..IR
Retrocopy VLIMALLTAAGAAAAAIVYVAHSGNRRANWVPICMQFHGFCQRTSGSVVATFLAVLVFIVLILMAACVIR

Parental  K
          .
Retrocopy R

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_31 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.

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Sorghum bicolor	Sb06g033470	1 retrocopy	retro_sbic_31 ,
Setaria italica	Si023150m.g	1 retrocopy	retro_sita_8,