RetrogeneDB ID: retro_sbic_26

Retrocopy location

• Organism: Sorghum (Sorghum bicolor)
• Coordinates: 4:4074994..4076082(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Sb04g004290
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Sb09g003710
• Aliases: None
• Description: None

Sequence

>retro_sbic_26
ATGGAGGGAGGCGGGAGCGCGGCGAAAGGGCCGGTGGTGGTGACGGGGGCGTCGGGCTTCGTCGGCTCCTGGCTCGTCAT
GAAGCTCCTCCAGGCCGGCTACACCGTCCGGGCGACCGTGCGCGATCCCGCGAACGCTGCCAAGACGAAGCCATTGCTGG
ACCTTCCCGGAGCAACGGAGCGCCTGTCCATATGGAAAGCCGACCTGGCGGAGGAAGGCAGCTTCGACGACGCCATCAGG
GGCTGCACCGGCGTCTTCCACGTCGCCACGCCCTTGGACTTCGAGTCCCAAGACCCCGAGAACGAGGTGATCAAGCCGGC
GGTGGAAGGGGTGATCAGCATCTTGCGAGCCTGCAAGGAGGCCGCCGCCGCCGGCGGCGGCACCGTGCGCCGCGTCGTCT
TCACTTCCTCCGCCGGGACGTGCAGCGTCGAGGAGCGGCAGAGGCCCGTCTACGGCGACGACGACTGGAGCGACGTCGAT
TTCTGCCGTCGCGCCAAGATGACCGGGTGGATGTACTTCGTGTCCAAGACCCTGGCGGAGAAGGCGGCGCTGGCGTACGC
GGCGGAGCACGGCGTGGACCTCGTCAGCATCATCCCGACGCTCGTCGTCGGCCCTTTCGTCAGCTCCGGCATGCCGCCCA
GCCTCGTCACCGCGCTGGCGCTCGTCACGGGGAACGAGGCACACTACTCGATCCTGAAGCAGGTGCAGTTCGTCCACCTC
GACGACCTCTGCGACGCCGAGATCTTCCTCTTCGAGCACCCGGCCGCCGCCGCCGGACGCTACGTCTGCTCCTCGCACGA
TGCCACCATCCACGGCCTCGCCGCCATGCTCAGGGATAGGTACCCCGAGTACGACATCCCGCAGAGGTTCCCTGGGATCG
AGGACGACCTCCAGCCAGTGCGCTTCTCGTCCAAGAAGCTCCTAGACCATGGGTTCACTTTCAAGTACACGGCAATGGAG
GACATGTTCGACGCAGCCATCCGGACGTGCCGGGAGAAGGGCCTCATCCCCCTCGCCACTGCCGGAGGCGGAGGGGACGA
CTCTGCCTCAGTGCGCGCACCTGGCGAGACGGATGTGACGATTGTTTG

Alignment

ORF - retro_sbic_26 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.11 %
• Parental protein coverage: 98.34 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IEGGASATKGPVVVTGASGFVGSWLVMKLLHAGYTVRATVRDPANVEKTKPLLDLPGATERLSLWKADLA
          .EGG.SA.KGPVVVTGASGFVGSWLVMKLL.AGYTVRATVRDPAN..KTKPLLDLPGATERLS.WKADLA
Retrocopy MEGGGSAAKGPVVVTGASGFVGSWLVMKLLQAGYTVRATVRDPANAAKTKPLLDLPGATERLSIWKADLA

Parental  VEGSFDDAIRGCTGVFHVATPMDFESKDPENEVIKPTVEGMISIMQACKEA----GTVRRIVFTSSAGTV
          .EGSFDDAIRGCTGVFHVATP.DFES.DPENEVIKP.VEG.ISI..ACKEA....G...R.V...S....
Retrocopy EEGSFDDAIRGCTGVFHVATPLDFESQDPENEVIKPAVEGVISILRACKEAAAAGGGTVRRVVFTSSAGT

Parental  NVEERRK-PVYDEDSWTDVDFCRRVKMTGWMYFVSKTLAEKAAMAYAAEHGVDLITVIPTLVVGPFLSAG
          ...E.R..PVY..D.W.DVDFCRR.KMTGWMYFVSKTLAEKAA.AYAAEHGVDL...IPTLVVGPF.S.G
Retrocopy CSVEERQRPVYGDDDWSDVDFCRRAKMTGWMYFVSKTLAEKAALAYAAEHGVDLVSIIPTLVVGPFVSSG

Parental  MPPSLVTAMALVTGNEAHYSILKQVQFIHLDDLCDAHLFLFEHP-AAAGRYVCSAADATIHGLAAMLRER
          MPPSLVTA.ALVTGNEAHYSILKQVQF.HLDDLCDA..FLFEHP.AAAGRYVCS..DATIHGLAAMLR.R
Retrocopy MPPSLVTALALVTGNEAHYSILKQVQFVHLDDLCDAEIFLFEHPAAAAGRYVCSSHDATIHGLAAMLRDR

Parental  YPEYNIPRRFPGIDDDLQLVRFSSKKLLDHGFTFRYTTMENMYDAAIRTCREKGLIPLATAGGEGGSASA
          YPEY.IP.RFPGI.DDLQ.VRFSSKKLLDHGFTF.YT.ME.M.DAAIRTCREKGLIPLATAGG.GG..SA
Retrocopy YPEYDIPQRFPGIEDDLQPVRFSSKKLLDHGFTFKYTAMEDMFDAAIRTCREKGLIPLATAGG-GGDDSA

Parental  GAPGPGGTDAAI
          ....PG.TD..I
Retrocopy SVRAPGETDVTI

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_26 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	Sb09g003710	1 retrocopy	retro_sbic_26 ,