RetrogeneDB ID: retro_gmax_27

Retrocopy location

• Organism: Soybean (Glycine max)
• Coordinates: 14:25268479..25268939(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: GLYMA20G26480
• Aliases: None
• Description: None

Sequence

>retro_gmax_27
GTTCTCAGTGAAGGCTTAGTTTCTGATGTGGTGTTGTGGATGAATTGGCGTGGAGCAATTGCGGTGCTTATTTCTGCCAC
CGCATTGTGGTACCTCTTCGAGCGTGCTGCTTACAATTTCTTGTTCTTCATCGCCAATGTCGTGTTGCTTCTCATCGTTA
TTTTTTTTCTGGGCCAAAGCTGCTAACCTTCTCAATAGACCTCTTCCTCCTCTCCCCGATCTAGAGATCTCGAAGGAAAC
TATTGTCAGGGTTGTTGATGCACTGCAAATTTGGTTGCATCTAGCCTTGTCCATTGCACATGACATAGCAATTGAGAACA
ATTTTCTACTTTTCCTCCAGGTTGTTGGTGTATTGTGGGTAATATCTTACATCTGTAGTTTGTTCAACTTTTTGACTTTG
ATATATATTGGTGTTCTTCTTCGCTTGTCTCTCCCTGTGTTGTATGACAAGTACCAGAAT

Alignment

ORF - retro_gmax_27 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.29 %
• Parental protein coverage: 75.49 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VLGEGLVADVVLWKNWRGAVAVLVSATTLWYLFERAGYNFLSFVANVVLLLV-AILFFWAKAANLLNRPL
          VL.EGLV.DVVLW.NWRGA.AVL.SAT.LWYLFERA.YNFL.F.ANVV.LL.......WAKAANLLNRPL
Retrocopy VLSEGLVSDVVLWMNWRGAIAVLISATALWYLFERAAYNFLFFIANVV-LLL>SLXXXWAKAANLLNRPL

Parental  PPLPDLEISEETIARVADALQIWLNRALSVAHDIAIERNLLLCLQVVGVLWVISYIGSLFNFLTLIYIGV
          PPLPDLEIS.ETI.RV.DALQIWL..ALS.AHDIAIE.N.LL.LQVVGVLWVISYI.SLFNFLTLIYIGV
Retrocopy PPLPDLEISKETIVRVVDALQIWLHLALSIAHDIAIENNFLLFLQVVGVLWVISYICSLFNFLTLIYIGV

Parental  LLSLSLPVLYDKYQD
          LL.LSLPVLYDKYQ.
Retrocopy LLRLSLPVLYDKYQN

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_27 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Glycine max	GLYMA20G26480	1 retrocopy	retro_gmax_27 ,
Vitis vinifera	VIT_03s0180g00170	1 retrocopy	retro_vvin_192,