RetrogeneDB ID: retro_sbic_1

Retrocopy location

• Organism: Sorghum (Sorghum bicolor)
• Coordinates: 4:5228557..5229504(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Sb04g005360
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Sb02g025100
• Aliases: None
• Description: None

Sequence

>retro_sbic_1
ATGACGACGGCGACGACGACTAAGCCGGCGGCGGAACGCAGCGGGCGGCGCTACGCGCTGCTGCTGGCGCTCTGGGACTC
GGAGTACGCCAAGGAGGTGTACGGCGGGTACTACACCGTCTTCGTCTCCGCGTTCGGCGACGGCGCCAGCGGTGGCACCG
ACGAGAGGTGGGACTCCTTCCGCGTGATCGCCGGCGAGTTCCCGGCGCCGGAGGACCTGGCGTCGTACGACGGCTTCGTG
GTGAGCGGCAGCCCGCACGACGCGCACGGCGACGAGCCGTGGATCCGGCGCCTCTGCGCGCTCGTCCAGACCGTCCACGC
CATGAGGAAGCGTGTGCTCGGCGTCTGCTTCGGGCACCAGGTCCTGTGCCGAGCGCTGGGCGGAAGGGTCGGCAGGGCAC
GGAACGGCTGGGACGTCGGGGTGAGGAAGGTGACGTTTGCGCCGGACCTCCTGGAGGGCCGCCTCGAGTTCCTCATCGGG
GATCTCGTCGCCGATGAGCTTCCGGCCCAGAGCGCCGGCCTCATCGAGGTTCACCAGGACGAGGTGTGGGAGATCCCGCC
GGCGGCGACGGTGCTGGCCTACTCGGAGAAGACGCGCGTGGAGGTGTTCGCGGTCGGGGAGCACGCGCTGGGCATCCAGG
GACACCCGGAGTACACCGTCGACATCCTCCACAACCTCATCGACCGCCTCACCGGCCAGAAGGCCATCCGGAGGAGCGTC
GGCGAGGAGGCACGGCGGACGGTCGCGGAGACCGGCGGGCCGGACCGCGCGTTCTGGACGGCGCTCTGCAAGGGTTTTCT
CCGGGGCGGAGGAGATCGTACGCAGCCTGCTCTGCCGGCGATGCGGGAGACGACGGCGGCGCCGGAGGTGACCAGCTGCG
CCGTCGCTGGCTGCGGCTTCACCAGCGCAGGCGCAGCTGCAATGATCCAGTTGGCTCGCAGCAACTA

Alignment

ORF - retro_sbic_1 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.56 %
• Parental protein coverage: 82.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AFGDAGETWDLYRAIDGELPAPDEVQCYDGFVISGSPHDAYADDLWILRLCRLVRALHGMRKRVLGVCFG
          A.G...E.WD..R.I.GE.PAP.....YDGFV.SGSPHDA..D..WI.RLC.LV...H.MRKRVLGVCFG
Retrocopy ASGGTDERWDSFRVIAGEFPAPEDLASYDGFVVSGSPHDAHGDEPWIRRLCALVQTVHAMRKRVLGVCFG

Parental  HQVICRALGGRVGKARAGWDVGVREVAIAEAPAPALPPRRFLDALRECDQLPPR-AKITEVHQDEVWEVP
          HQV.CRALGGRVG.AR.GWDVGVR.V....AP........FL......D.LP...A...EVHQDEVWE.P
Retrocopy HQVLCRALGGRVGRARNGWDVGVRKVTF--APDLLEGRLEFLIGDLVADELPAQSAGLIEVHQDEVWEIP

Parental  EGAEVLASSDKTGVEMFCVGEHMLGIQGHPEYTKDILLSLVDRLLAAGSITIPFAEAVKWQV-ETTAPDR
          ..A.VLA.S.KT.VE.F.VGEH.LGIQGHPEYT.DIL..L.DRL.....I.....E.....V.ET..PDR
Retrocopy PAATVLAYSEKTRVEVFAVGEHALGIQGHPEYTVDILHNLIDRLTGQKAIRRSVGEEARRTVAETGGPDR

Parental  EFWLKLCKSFLK
          .FW..LCK.FL.
Retrocopy AFWTALCKGFLR

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_1 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	Sb02g025100	1 retrocopy	retro_sbic_1 ,