RetrogeneDB ID: retro_sbic_22

Retrocopy location

• Organism: Sorghum (Sorghum bicolor)
• Coordinates: 4:6234474..6235169(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Sb04g006270
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Sb03g030950
• Aliases: None
• Description: None

Sequence

>retro_sbic_22
ATGGCCACCACCACCACCACGGCGACAGCGTCCCTCACCACCCTGTCCCCCGCCGGCGTCGGCAAGCGGTTCGTCCTCTC
GTCCCCGCCCCTCTCATTCTCCTCTCACCGCCTGACCGCCGGCCTCCGCCACCGCCACCGCGGCGGCGCGGCGTCGAGGA
CGGCGAGGAGGCGGGCGGCGTCGGCGTCCCCGGTGGTGGCGACCATCGCGGTGGGCGACAAGCTCCCCGACGCGACGCTG
TCCTACTTCGACCCGTCCGACGGGGAGCTGAAGACGGTGACGGTGGCGGAGCTGACGGCGGGCAAGAAGGCCATCCTCTT
CGCGGTGCCCGGCGCGTTCACGCCCACGTGCTCGCAGAAGCACCTGCCGGGGTTCGTGGAGAAGGCCGGCGAGCTCAAGG
CCAAGGGCGTGGAGACCGTGGCGTGCGTGTCGGTGAACGACGCGTTCGTGATGAAGGCGTGGAAGGAGGCGCTGGGGCTC
GGCGAGGATGTGACGTTGCTGTCGGACGGCAACCTGGAGCTGACACGCGCGCTGGGCGTCGAGATGGACCTCTCCGATAA
GCCCGTCGGGCTCGGCGTCCGGTCCAGGAGGTACGCGCTCCTGGCCGAGGACGGCGTCGTCAAGGTGCTCAACCTCGAGG
ACGGCGGCGCCTTCACCACCAGCAGCGCCGAGGAGATGCTCAAGGTGCTCGGCTG

Alignment

ORF - retro_sbic_22 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.36 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAPIAVGDSLPDGQLGWFDEND-QLQQVSVHALAAGKKVILFGVPGAFTPTCSNQHVPGFITQAEQLKAK
          .A.IAVGD.LPD..L..FD..D..L..V.V..L.AGKK.ILF.VPGAFTPTCS..H.PGF...A..LKAK
Retrocopy VATIAVGDKLPDATLSYFDPSDGELKTVTVAELTAGKKAILFAVPGAFTPTCSQKHLPGFVEKAGELKAK

Parental  GVDEILLISVNDPFVMKAWAKTYPENKHVKFLADGSGAYTKALDLELDLTEK--GLGVRSKRFALLADDL
          GV......SVND.FVMKAW.........V..L.DG....T.AL..E.DL..K..GLGVRS.R.ALLA.D.
Retrocopy GVETVACVSVNDAFVMKAWKEALGLGEDVTLLSDGNLELTRALGVEMDLSDKPVGLGVRSRRYALLAEDG

Parental  KVTVANIEEGGQFTISGAEEILKAL
          .V.V.N.E.GG.FT.S.AEE.LK.L
Retrocopy VVKVLNLEDGGAFTTSSAEEMLKVL

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_22 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 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Arabidopsis thaliana	AT1G65980	1 retrocopy	retro_atha_13,
Arabidopsis lyrata	fgenesh2_kg.2__836__AT1G65980.1	1 retrocopy	retro_alyr_5,
Glycine max	GLYMA07G09240	1 retrocopy	retro_gmax_12,
Hordeum vulgare	MLOC_12954	1 retrocopy	retro_hvul_9,
Populus trichocarpa	POPTR_0018s09030	1 retrocopy	retro_ptri_12,
Prunus persica	PRUPE_ppa012586mg	1 retrocopy	retro_pper_22,
Sorghum bicolor	Sb03g030950	1 retrocopy	retro_sbic_22 ,
Selaginella moellendorffii	SELMODRAFT_159225	1 retrocopy	retro_smoe_4,
Solanum lycopersicum	Solyc07g020860.2	1 retrocopy	retro_slyc_41,
Theobroma cacao	TCM_028816	1 retrocopy	retro_tcac_8,