RetrogeneDB ID: retro_sbic_35

Retrocopy location

• Organism: Sorghum (Sorghum bicolor)
• Coordinates: 9:56398177..56399112(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Sb09g027310
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Sb02g031020
• Aliases: None
• Description: None

Sequence

>retro_sbic_35
ATGGCTGACGAGTCGGTCTACTGCCCGGACTGCCACCGCACGACCGAGGTGGTGCTGGACCACGCCACCGGCGACACAAT
CTGCACCGAGTGCGCGCTCGTCCTGGAGGCGCACTACATCGACGAGGGCTCCGAGTGGCGCAACTTCGCGGACGACGGCG
GCGGCGAGGACCGCGACCCCAGCCGCGTCGGCGGGCCCAGCGACCCGTTCCTCTCCAACACGCCGCTCGTCACCCGAATC
GCCTACGCCGGCCCGCAGAAGACGCAGGGCGAGGGCGGCCACGCGCTTCCGAGAATGCGGGTCAGCGCCGGCGCCGGCGG
CGCGGACCACGAGCAGGCGCTGGTGGATGCGTTCCACGCCATCGCGGACATGGCGGACCGCCTCGGCCTCGTCGGCACCA
TCCGGGACCGCGCCAAGGACGTCTACAAGAGGCTGGACGAGGCCAAGGCGTGCCCCACCAGGGGCAAGAAGCGGGACGTG
TTCTACGCCGCGTGCCTCTACGTCGCGTGCCGCAACGAGGGCAAGCCGCGCACTTACAAGGAGCTGGCCACGGTCACCGC
CGCCGGCGCCTCCGCCAAGAAGGAGATCGGCAAGATGACCACGCTCATCAAGAAGGTGCTCGGGGAGGAGGCCGGGCAGG
TGATGGACATCGGCGTCGTGCGCGCCGCCGACTACATGCGCCGCTTCTGCTCCCGGCTCGGGATGGGCAACCAGGAGATG
CGCGCCGCGCAGGAGGCCGCGCGGAGGCTCGAGAACGGCCTCGACGTGCGGCGCAACCCCGAGTCCATCGCGGCCGCCAT
CAGCTACATGGTCGTGCAGCGCGCCGGCGCCGGCAAGACCGTCCGTGACGTGTCCATGGCCACCGGCGTCGCCGAGGCCA
CCATCAAGGAGGCGCACAAGGACCTCACTCCGCACGCGGAGATGCTCTTCGCCTA

Alignment

ORF - retro_sbic_35 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.74 %
• Parental protein coverage: 63.46 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GSNPDRSLILAFRTIANMADRLGLVATIKDRANEIYKKVEDLKSI--RGRNQDAILAACLYIACRQEDRP
          G......L..AF..IA.MADRLGLV.TI.DRA...YK.....K....RG...D...AACLY.ACR.E..P
Retrocopy GADHEQALVDAFHAIADMADRLGLVGTIRDRAKDVYKRLDEAKACPTRGKKRDVFYAACLYVACRNEGKP

Parental  RTVKEICSV--ANGATKKEIGRAKEFIVKQLEVEMGQSMEMGTIHAGDFLRRFCSTLGMNNQAVKAAQEA
          RT.KE...V..A....KKEIG.....I.K.L..E.GQ.M..G...A.D..RRFCS.LGM.NQ...AAQEA
Retrocopy RTYKELATVTAAGASAKKEIGKMTTLIKKVLGEEAGQVMDIGVVRAADYMRRFCSRLGMGNQEMRAAQEA

Parental  VQRSEE-LDIRRSPISIAAAVIYMITQLSEDKKPLKDISLATGVAEGTIRNSYKDLYPYAARL
          ..R.E..LD.RR.P.SIAAA..YM..Q.....K...D.S.ATGVAE.TI....KDL.P.A..L
Retrocopy ARRLENGLDVRRNPESIAAAISYMVVQRAGAGKTVRDVSMATGVAEATIKEAHKDLTPHAEML

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_35 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Brachypodium distachyon	BRADI4G36290	1 retrocopy	retro_bdis_39,
Aegilops tauschii	F775_29675	1 retrocopy	retro_atau_5,
Hordeum vulgare	MLOC_10647	1 retrocopy	retro_hvul_45,
Medicago truncatula	MTR_7g091230	2 retrocopies	retro_mtru_26, retro_mtru_3,
Sorghum bicolor	Sb02g031020	1 retrocopy	retro_sbic_35 ,