RetrogeneDB ID: retro_gmax_2

Retrocopy location

• Organism: Soybean (Glycine max)
• Coordinates: 13:44282438..44284199(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: GLYMA13G44970
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: GLYMA07G00540
• Aliases: None
• Description: None

Sequence

>retro_gmax_2
ATGGCGTGTACCAAAGCGACCTTCACCTTTTCACAGTACTGTAGCGACAGGTGCAGCAGCAGCAGAAGAAGAAGAAGAGC
CTCTGCTGTTTCATTCTTCAACGGCAATTCGGTCATGAGGCTCTCCTCTCATCGCGGCGCCTTGCTTACGAACAATGTTT
TGGAGACGTCCAAGTCTAAGGACAAGAGCAGCAGCAACAATAATATTATATTGGTGAGCGAGAAACTTGGTGAAGCAGGG
CTTAAAGTGCTACGCGAATGGGGCGACGTTGAATGCGCGTACGATCTCTCACCCGAGGAGCTCTGCTCAAAGATCTCATG
TTGCGACGCTTTAATCGTGAGGAGCGCCACCAAGGTCACAAGAGAGGTCTTCCAAGCTTCCAAAGGAAGATTAAAGGTTG
TGGGAAGAGCTGGTGTAGGCATTGACAACGTGGACCTCCAGGCTGCCACCGAGTTTGGTTGCATCGTCGTCAACGCACCC
ACCTCCAACACTGTCGCTGCTGCAGAGCTTGCCATCGCGCACCTTGCTGCCATGGCAAGAAACGTTGCCAGGGCTGATGC
CTCCATGAAAGCTTCCAAGTGGGAGAGAAACAAGTACGTTGGTGTTTCTATGGTTGGGAAGACAGTGGCGATAATGGGAT
TTGGAAAAGTGGGATATGAAGTGGCGCGGCGTGCAAAAGCAGCGTTGGGAATGAACGTGGTTGCGCATGATCCCTATGCC
TCTGCGGACAGAGCGAGTGCTATTGGGGTCCATCTTGTGTCCTTCGATGAGGCCATCTCCAACGCGGATTTCATCTCTCT
CCACATGCCACTCATTCCTTCCACCCACAAGATATTCAACCACACTAGTTTCGCAAAGATGAAGAGAGGAGCGCGCATCA
TCAACGTCGCGAGAGGCGGAGTGATCGACGAAGATGACTTGGTAAGAGCCCTGGACGATGGAACAGTTGCTGAGGCAGCA
CTTGATGTGTTCACGGAGGAGCCCCCGGCCAAAGATAGCAAGTTAGTGAAGCACGAGAAAGTGACGGTAACACCTCACCT
TGGAGGAAGCACAAAAGAGGCACAGGAGGGTGTGGCCATTGAAATAGCAGAGGCTGTAATGGGAGCATTGAAGGGGGAAC
TTTCAGCCAGAGCTGTGAATGCTCCAGCGGTTCCAACCGAGCTGGTCGCAGAACTGGCTCCATATGTCGTGCTGGCAGAG
AAGCTGGGGCGGGTAGCTGTGCAGTTGGTATCAGAATCAAGAGATGTGAAGGTGGTTTATCGATCAGCTGATTTGGACAC
TAGACTTTTGCGAGCCATGATCATAAAAGGCCTCATTGAACCCACGTCCAATTCAGCCATCAACTTGGTAAATGCTGACT
TCATTGCCAAGGAGAAGGGGGTTCGCATAAGCGAGGAAATAATAGCTGGCGTGGAACTAATTGATTCAATCCAGCTACAG
ATATCAAATGTAATTAGCATAGAGGGAAAAGTCAAGTACGGTAGCCCCCACCTCACACGTGTGGGCTCCTTTGATGTCGA
TGTGAGCTTAGAGGGGAACCTTATACTGTACCGGCAGGTGGATCAGCCAGGTATGATTGGGCGCGTTGGAACTATACTGG
GTCAGCACAACATCAATGTTAGCTTTATGAGTTTGGGAAGGACATGTCGGAGAAAGATGGCTATTGTGGCTATTGGTGTC
GATGAAGAACCAAGCAAGGAAGCTCTTCAACATATAGGATCGCTTCCTGCTATCCAAGACTTAGTCTTTCTCAAACTCTA
G

Alignment

ORF - retro_gmax_2 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.65 %
• Parental protein coverage: 68.06 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TQTSLRRSNSEDVGSLGEKPTILVSEKLGEAGLQVLRGVGHVECAYELSQEELCTKISCCDALIVRSGTK
          T...L..S.S.D..S......ILVSEKLGEAGL.VLR..G.VECAY.LS.EELC.KISCCDALIVRS.TK
Retrocopy TNNVLETSKSKDKSSSNNN-IILVSEKLGEAGLKVLREWGDVECAYDLSPEELCSKISCCDALIVRSATK

Parental  VTREVFEAGKGRLKVVGRAGVGIDNVDLQAATEFGCLVVNAPTANTIAAAEHGIALLAAMARNVAQADAS
          VTREVF.A.KGRLKVVGRAGVGIDNVDLQAATEFGC.VVNAPT.NT.AAAE..IA.LAAMARNVA.ADAS
Retrocopy VTREVFQASKGRLKVVGRAGVGIDNVDLQAATEFGCIVVNAPTSNTVAAAELAIAHLAAMARNVARADAS

Parental  TKAGKWQRSKYVGVSMVGKTLAVMGFGKVGSEVARRAKG-LGMHVIAHDPYAPADRARAIGVDLVSFDHA
          .KA.KW.R.KYVGVSMVGKT.A.MGFGKVG.EVARRAK..LGM.V.AHDPYA.ADRA.AIGV.LVSFD.A
Retrocopy MKASKWERNKYVGVSMVGKTVAIMGFGKVGYEVARRAKAALGMNVVAHDPYASADRASAIGVHLVSFDEA

Parental  IATADFISLHMPLTPTTNKIFNDNTFAKMKKGVRIVNVARGGVIDEDALVRALDTGIVAQAALDVFTEEP
          I..ADFISLHMPL.P.T.KIFN...FAKMK.G.RI.NVARGGVIDED.LVRALD.G.VA.AALDVFTEEP
Retrocopy ISNADFISLHMPLIPSTHKIFNHTSFAKMKRGARIINVARGGVIDEDDLVRALDDGTVAEAALDVFTEEP

Parental  PSKDSKLVQHENVTVTPHLGASTKEAQEGVAIEIAEAVLGALKGELSATAVNAPMVAPEVLSELAPYVVL
          P.KDSKLV.HE.VTVTPHLG.STKEAQEGVAIEIAEAV.GALKGELSA.AVNAP.V..E...ELAPYVVL
Retrocopy PAKDSKLVKHEKVTVTPHLGGSTKEAQEGVAIEIAEAVMGALKGELSARAVNAPAVPTELVAELAPYVVL

Parental  AEKLGRLAVQLVCGGSGIKSVKIVYRSARGPDDLDTRLLRAMVTKGLIEPISNTIVNLVNADFIAKQKGL
          AEKLGR.AVQLV...S....VK.VYRSA....DLDTRLLRAM..KGLIEP.SN...NLVNADFIAK.KG.
Retrocopy AEKLGRVAVQLV---SESRDVKVVYRSA----DLDTRLLRAMIIKGLIEPTSNSAINLVNADFIAKEKGV

Parental  RISEE
          RISEE
Retrocopy RISEE

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_2 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.

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Glycine max	GLYMA07G00540	1 retrocopy	retro_gmax_2 ,