RetrogeneDB ID: retro_sbic_28

Retrocopy location

• Organism: Sorghum (Sorghum bicolor)
• Coordinates: 2:77657785..77658481(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Sb02g043850
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Sb01g038100
• Aliases: None
• Description: None

Sequence

>retro_sbic_28
ATGGCGATGACCACTACCACCACCACCACCACCACACCCAAAAGCACCAGCAGCAGCCCCGGCGCGTACGTCGCCAAGCC
TCCCCCGCCGCCGCCGGGCTACGTCGACGTCGTCCACAACAAGGCGGCGCCGGCGGCGTACGATTCCTACAACGGACGAC
GACAAGGAGGCGGCGCGGCGGCCACGGCCACCAGCAGGGCCTCCTCCGACTACGACGAAGACCGTTACCAGCAGCAGGCG
GCGGCGGGAGCGCGGGCGCTGGACGGGCTCCTGCTGCTGCTGCGCGCGGCCGCGTCGGTCATGTCGTTCGTGGCCGTCGC
GCTCGTCGCGTCCTGCCGCCACGGCGACTGGATGGAGTTCGCGCGCTACCCGGAGTACAGGTGCCTCCTGGGGGCCTCCG
TGCTCGCCTGCGTCTACGCCGCCGCGCAGGCGCTTCGGGTCTTCCGACGGATGCGCGCCGCCGGCTACGGCGGGAGATCG
GGAGGCGGAGGCGGCCTCGCGGATTTCGCCGGCGATCAGGTGGTGGCGTATCTGCTCATCGCGGCGTCGGCGGCGGCTCT
CCCCATCACCCTCCGCATGAGATCCGCCGTCCTCAACGTCTTCACGGACGCCATGACGGCCGCCATCAGCCTCGGTTTCA
TCGCCTTTGCAGCGCTCGCCTTGTCCGCCATGCTCTCCGGATTCTTCACACTCTAG

Alignment

ORF - retro_sbic_28 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.75 %
• Parental protein coverage: 64.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LDKSPLALHAAAAIFAFVALVLVASNQHGDWMQFDRYQEYRYLLAIASLALLYSLAQAARHAHRMRG-GV
          LD...L.L.AAA....FVA..LVAS..HGDWM.F.RY.EYR.LL....LA..Y..AQA.R...RMR..G.
Retrocopy LDGLLLLLRAAASVMSFVAVALVASCRHGDWMEFARYPEYRCLLGASVLACVYAAAQALRVFRRMRAAGY

Parental  DPVSSASARLLDFVGDQVVAYLLMSALSAAVPITNRMRSAVVNNFTDATAAAISMAFFSFVALALSAVVS
          ...S.....L.DF.GDQVVAYLL..A..AA.PIT.RMRSAV.N.FTDA..AAIS..F..F.ALALSA..S
Retrocopy GGRSGGGGGLADFAGDQVVAYLLIAASAAALPITLRMRSAVLNVFTDAMTAAISLGFIAFAALALSAMLS

Parental  GY
          G.
Retrocopy GF

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_28 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	GRMZM2G007475	1 retrocopy	retro_zmay_8,
Leersia perrieri	LPERR03G12390	1 retrocopy	retro_lper_2,
Sorghum bicolor	Sb01g038100	1 retrocopy	retro_sbic_28 ,