RetrogeneDB ID: retro_gmax_17

Retrocopy location

• Organism: Soybean (Glycine max)
• Coordinates: 1:47347772..47348576(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: GLYMA20G32790
• Aliases: None
• Description: None

Sequence

>retro_gmax_17
CACCGATAGCCCCCCTGCCTCAAACTGAAGCCCAAACCAACGTCGTGCAAGTGTAATTATTCCATTGTGAATGTGCAGAC
TTATGGGGTTGGCTTGTGGTACACTTGGTTTGATAGGGATTTGAGTGTTGCTGGAAGGGTCATTCTCAGAATTGGCCATA
ATTCTTATGTGCTTAAGCTTCTCAAAGTAGATAGACCCATGTTGCGCATTCCCACATTGACCATTCATCTTGATCGCACA
GGGAATCAGGATGATTTTAAACCAAATCTAGAGACTCATCTTCTTCATTTACTCTCAATGGAACCTGAGGGAACTTCTTT
GGAATTCAACTCCAAAGAGAAGAATAGTGCCTTGCCATCCAAAGCTCATCATCATCGAGTGCTTATGTAGGTACTGTCAG
ATGAGTTAAACGGTAATGTTGATGACATAGTGAATATTGAACTGAATGTTTGTGATACTCAACCTAGCTGCCTTGGAGGT
GGAAACAATGAATTTATTTTTTCTGGAAGATTAGATAATCAGGCTTCAAGTTATTGTGCATTAAGGGCACTTGTTGACTC
ACGTGAATCTCCTGGTGACTTAGCAAGTGAAAATGCAATTTGAATGATTGCTTTATTTGACAATGAAGAGGTGGGTTCAG
GTTTTGTTCAAGGAGCTGGAGCACCCACCATGTTTCAGGCCATGAGACGTATATTAGCAAATAACTATGTTGGTGAAGGC
TCTTTTGTGCGCACTATTTGCCAATCATTTATTGTGTCTGTAGATAAGGCCCATGGAGTTCATCCTAATTTTATGGATAA
ACAT

Alignment

ORF - retro_gmax_17 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.39 %
• Parental protein coverage: 50.28 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  HTDSPCLKLKPKTASCKCNYSMVNVQTYGAGLWYTWFDRDLSVAGRVILRSSHNSYVHKLVKINRPILRI
          H...PCLKLKPK..SCKCNYS.VNVQTYG.GLWYTWFDRDLSVAGRVILR..HNSYV.KL.K..RP.LRI
Retrocopy HR*PPCLKLKPKPTSCKCNYSIVNVQTYGVGLWYTWFDRDLSVAGRVILRIGHNSYVLKLLKVDRPMLRI

Parental  PTLAIHLDRTVNQDGFKPNLETHLHPLLSMKPEDTSLESNSKEKNSALSSKAHHHRLLMQVLSDELNCDI
          PTL.IHLDRT.NQD.FKPNLETHL..LLSM.PE.TSLE.NSKEKNSAL.SKAHHHR.LM.VLSDELN...
Retrocopy PTLTIHLDRTGNQDDFKPNLETHLLHLLSMEPEGTSLEFNSKEKNSALPSKAHHHRVLM*VLSDELNGNV

Parental  DDIVNIELNVCDTQPSCLGGGNNEFIFSGRLDNLASSYCALRALIDSCQSPGDLASESAIRMVALFDNEE
          DDIVNIELNVCDTQPSCLGGGNNEFIFSGRLDN.ASSYCALRAL.DS..SPGDLASE.AI.M.ALFDNEE
Retrocopy DDIVNIELNVCDTQPSCLGGGNNEFIFSGRLDNQASSYCALRALVDSRESPGDLASENAI*MIALFDNEE

Parental  VGSGSVQGAGAPTMFQAMRRIVGDLANNYVSEGSFERTIRQSFLVSADMAHGVHPNFMDKH
          VGSG.VQGAGAPTMFQAMRRI...LANNYV.EGSF.RTI.QSF.VS.D.AHGVHPNFMDKH
Retrocopy VGSGFVQGAGAPTMFQAMRRI---LANNYVGEGSFVRTICQSFIVSVDKAHGVHPNFMDKH

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Glycine max was not studied using RNA-Seq expression data.

ChIP-Seq

Glycine max was not studied using ChIP-Seq data.

EST

Glycine max was not studied using EST data.

TSS

Glycine max was not studied using FANTOM5 data.

Lab

retro_gmax_17 was not experimentally validated.

Homology

Retrocopy orthology:

Glycine max 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
Glycine max	GLYMA20G32790	1 retrocopy	retro_gmax_17 ,