RetrogeneDB ID: retro_sbic_32

Retrocopy location

• Organism: Sorghum (Sorghum bicolor)
• Coordinates: 6:6289746..6291366(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Sb06g003080
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Sb03g029810
• Aliases: None
• Description: None

Sequence

>retro_sbic_32
ATGACGCCGACCAGAAGCGCCCGCAAGCGCCCGCGGACGCCCGAGGTGGCTCCCCCGCCACGCAAGCGCCGCGACGGCGG
CATCTACGTCCCTCCGTACCGCGCCACCGACGACGAGTCCAGCTACGAGCGCCGCAGCTGGGACGCGCTGCGGAGGAGCA
TCACGGGGCTGGTGAACAAGGCGACCGCCGCCAACATCCGCCACGTGGCGCCGGAGCTCCTGTCGGAGAACCTGGTGCGA
GGCCGCGGCCTGCTCTGCCGCGCGCTCCTCCGTTCCCAGGCGGCCAGCACCAGCAGCGCCACGGCCTTCACGCCGGTCTT
CGCGGCGCTCGCCGCCGTCGCCAACGCCAGGCTCCCCTGCGTCGGCCGCCTCCTCCTGGCGCGCCTCGCGCTCCGCGCCA
CGCGCGCCCACGCCGCGGGCGACAAGCACCGGCTCGCCGCGTCCGCCACGTTCGTCGCGCACCTCGTCAACCAGGGCGTC
GCCACCGACCTGCTCGCGCTCCAGCTCCTCGCGCTCCTCCTCGACCGCCCCACCGACGGCGGCAGCGTCGAGGTCGCCGT
CGGACTCGTCACCCACTGCGGCGCCAAGCTCCAGGAGTCGTGCCCGCGCGGGCTCAGCGCCGTGTTCGACTCCCTGCGGA
GCGTCCTCCACGACGGCGATGTTGACAAGCGCGTCCAGTTCTTGATCGAGGATCTCTTCGCCATCCGGAAGGCGCAGTTC
CGGGCTCACCCTCCCGTCCAGCCGGAGCTGGATCTCATCGAGCCGGACGACCAGGTGACGCATCAGATAGAACTCGACGG
TGATCAGCTCGACCCGGAGTTCCATCTTGACGTGTTCGAGCCCAGCCCTTCCTTCGCGCAAGACGAGGCGGCATACGAGG
ACCTCAGGCGAACCATGCTCGGAGTCGGAGACGACGACAAGATCCAATCTTCTTCTCCTGATGACGAAGAAACCGACAGC
GACGACGACGCGTCAGAAACGGATCAGCCGCCGGCGGTCGTGGTCCGCGACCAGACCGACACCGATCTGATCAACCTTCG
GCGGACCATCTACCTGACAGTCATGTCGAGCGTCAGCGCCGAGGAAGCTGGAAACAAGCTCCTGTCGGTGGTGCGTTCCG
GCCAGGAGCCGGAGCTGTGCGCCATGCTCGTCGAGTGCTGCAGGAAGGCGAAGGCCTACACGAGCTACTACGGCGAGCTC
GGGCAGCGGCTGTGCGCCGTCGACCGCGCGTACCAAGCCGGCTTCGAGGCCTGCTTCGCGGGGCACTACGCGGCGGCGCA
CCGCATGACGACCGACGAGCTGCGCGCGTCCGCCAGGTTCTACGCGCACCTGCTGGCCGCCGCCGACGCGCTGCCCTGGC
GCGGCGCGCTGGGGCGCGTCCGGGTCACGGAGCAGGACACGACGTCGTCGTCGCGCATCTTCATCAAGTTGCTGTTCCTG
GACCTCGCCGAGAAGCTCGGGGTCCGGACGCTCAGCAAGAAGAGGAACGACGACGATGCGGACGTGCGGGACGTCCTGTT
CCCCAGAGACTGCGCCAGTAACACGCGGTTCGCCATTAATTTCTTCACGGCGATCGGCCTCGGAGGTGTCACCGAGGCCG
CGAGGAAGCTCATTGTGTGA

Alignment

ORF - retro_sbic_32 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.64 %
• Parental protein coverage: 63.13 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RDVEDKSSPEYQRLTWDALKKSINGLVNKVNATNIKNIVPELFAENLVRGRGLFCQSCIKSQMASPG---
          R...D.SS..Y.R..WDAL..SI.GLVNK..A.NI....PEL..ENLVRGRGL.C.....SQ.AS.....
Retrocopy RATDDESS--YERRSWDALRRSITGLVNKATAANIRHVAPELLSENLVRGRGLLCRALLRSQAASTSSAT

Parental  -FTDVFAALVAVVNTKFPEIGRLLLVRVVLQLKRAYKRNDKPQLLAATKFIAHLVNQVVAHELVALELLT
          .FT.VFAAL.AV.N...P..GRLLL.R..L...RA....DK..L.A...F.AHLVNQ.VA..L.AL.LL.
Retrocopy AFTPVFAALAAVANARLPCVGRLLLARLALRATRAHAAGDKHRLAASATFVAHLVNQGVATDLLALQLLA

Parental  VLLENPTDD-SVEVAVGFVKECGAMLQDLSPQGLHAIFERFRGILHEGEIDKRVQFLIEGLFAIRKAKFQ
          .LL..PTD..SVEVAVG.V..CGA.LQ...P.GL.A.F...R..LH.G..DKRVQFLIE.LFAIRKA.F.
Retrocopy LLLDRPTDGGSVEVAVGLVTHCGAKLQESCPRGLSAVFDSLRSVLHDGDVDKRVQFLIEDLFAIRKAQFR

Parental  GFPAIRPELDLVEQEDQFTHEISLE-DDLDPETNLNVFRANPNFVEDEKAYENLKRSILGAESSEDEEGS
          ..P...PELDL.E..DQ.TH.I.L..D.LDPE..L.VF...P.F..DE.AYE.L.R..LG.....D....
Retrocopy AHPPVQPELDLIEPDDQVTHQIELDGDQLDPEFHLDVFEPSPSFAQDEAAYEDLRRTMLGV--GDDDKIQ

Parental  DAASDDDEDEEESDEEDEEQ---MEIRDRTETNLVNLRRTIYLTIMSSVDFEEAGHKLMKIKLEPGQEME
          ....DD.E.....D.....Q......RD.T.T.L.NLRRTIYLT.MSSV..EEAG.KL.......GQE.E
Retrocopy SSSPDDEETDSDDDASETDQPPAVVVRDQTDTDLINLRRTIYLTVMSSVSAEEAGNKLLSV-VRSGQEPE

Parental  LCIMLLECCSQERTYLRYYGLLGQRFCMINKVYQENFEKCFVQQYSMIHRLETNKLRNVAKFFAHLL-GT
          LC.ML.ECC.....Y..YYG.LGQR.C.....YQ..FE.CF...Y...HR..T..LR..A.F.AHLL...
Retrocopy LCAMLVECCRKAKAYTSYYGELGQRLCAVDRAYQAGFEACFAGHYAAAHRMTTDELRASARFYAHLLAAA

Parental  DALPWH-VLAYIRLTEEDTTSSSRIFIKILFQELSEHLGIRLLNERLNDPNMQGSFESIFPKDHPKNTRF
          DALPW...L...R.TE.DTTSSSRIFIK.LF..L.E.LG.R.L....ND..........FP.D...NTRF
Retrocopy DALPWRGALGRVRVTEQDTTSSSRIFIKLLFLDLAEKLGVRTLSKKRNDDDADVR-DVLFPRDCASNTRF

Parental  SINFFTSIGLGGITESLREYL
          .INFFT.IGLGG.TE..R...
Retrocopy AINFFTAIGLGGVTEAARKLI

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_32 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Brachypodium distachyon	BRADI4G39400	1 retrocopy	retro_bdis_57,
Medicago truncatula	MTR_3g434840	1 retrocopy	retro_mtru_18,
Sorghum bicolor	Sb03g029810	1 retrocopy	retro_sbic_32 ,
Arabidopsis lyrata	scaffold_202963.1	1 retrocopy	retro_alyr_10,
Solanum lycopersicum	Solyc04g079920.2	1 retrocopy	retro_slyc_47,