RetrogeneDB ID: retro_gmax_38

Retrocopy location

• Organism: Soybean (Glycine max)
• Coordinates: 2:36293621..36294691(-)
• Located in intron of: GLYMA02G32980

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: GLYMA12G35670
• Aliases: None
• Description: None

Sequence

>retro_gmax_38
ACTTCTACGCAGCGCAAAGTCACGTTGATGGTTGCTTTTATATTTGCTGTTGTGTTTCTTATCTCATACTTCATTTCCTG
TGTCTTTAAACCTCCAATCGAGAAAACAAGAGTGGAGATATTAAACATGATGACTTAATAATATTAAGAATTTTTCAACT
TTTTGAGAAAGAAACTCTGCAAAAGATCCTGACCGAGGATAGGACTCCCAATGTTACTGCCATAAGTGGGCTGTATCATG
AAATTAGTCAACATGGGGGCAATGTCTTGTTAGCTTCTGAAGTTAAAGAGCTGTTGTTTGGGGTAAATTAACTGACAAAT
ATCAAAGAGGAACAAATAGCAGACTTGTTAAAAGTTTTTGACCAAAATGGTGATCAAATTATAACCAAGGAAGAGTATGT
CACTGACAACAAGAATACATTACCTAAACAAAGCCTGCTCTTGATAGTCAATACTTCCCCAAACAATCTGTGAACAAAAT
GTATCAGACTTTTATCAACCTATGGATTGAACAAGTGAGAAAAGAACACGAATTGAAGGGACATCTTATATCTGAAGTCT
TGAAGCATGCTTAGAATGATATGGTTGGAAGGTTGAGCAAAGATGATGGCTCACCTGATAAAATTGCTATCTGAAGGTTG
TTTGAGGAAATTGATGTCAACGGGTATAATCAAATTTCAAGATCTGAATTTGCAAAATTAGTCAAGTGCATCGAGTTTGG
CCAGGTTGTAGATGATGCTCAAGAGGCAGTTATTAAACTCGTTCAAGATTTGGATCTCAACCGAGACAATGAAATTAGTG
AGACTGAATTTGTTGATGGTCTTACAAAATGGATGAACTCAAATTCCAGACAAGCTGCTAACTCAAAATCTTCATCTCAG
GGAATTCATCAAACCTGGGAAGGTGCTGAAAAAGGGAATGGAAGAGAATCAAAGAATCAACCCTAAGTAGCATGTGGTGT
TGGGAGTTGCTATACTGTCTCTTCTTGCTGAACCGTTAATAGTGTCCAAAAATTCTCTGAAGAAGCAGGAGTTTTCATCA
TTTTTCATCTCATTCTTTTTAGTGTTCATT

Alignment

ORF - retro_gmax_38 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.03 %
• Parental protein coverage: 50.49 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SSIPRNVTLMVALTVAVAFLISYFIYQVFKPQIEKTRLEY-IKHDDLI-LRIFQRVEKQTLQKILTDDGT
          .S..R.VTLMVA...AV.FLISYFI..VFKP.IEKTR.E..IKHDDLI.LRIFQ..EK.TLQKILT.D.T
Retrocopy TSTQRKVTLMVAFIFAVVFLISYFISCVFKPPIEKTRVEI<IKHDDLIILRIFQLFEKETLQKILTEDRT

Parental  PNVAAISGLYHEISQRGGKDLLASEVKELLFGTKLNDTNIKEEQIADMLKVFDRNGDQIITKEEFVTG-L
          PNV.AISGLYHEISQ.GG..LLASEVKELLFG.....TNIKEEQIAD.LKVFD.NGDQIITKEE.VT...
Retrocopy PNVTAISGLYHEISQHGGNVLLASEVKELLFGVN*L-TNIKEEQIADLLKVFDQNGDQIITKEEYVTD<Q

Parental  TEYINQSKHALDRQYLPKESLNKMYQTFIKPWIEHVRKQRELKGHLISEVLKHAQNDMVGRLRQDDGTPD
          .EYI...K.ALD.QY.PK.S.NKMYQTFI..WIE.VRK..ELKGHLISEVLKHA.NDMVGRL..DDG.PD
Retrocopy QEYIT*TKPALDSQYFPKQSVNKMYQTFINLWIEQVRKEHELKGHLISEVLKHA*NDMVGRLSKDDGSPD

Parental  KIAIKRLFEEIDVNQDNHISRSELEKVVKDIQFGKAV-ETEEAVTKLVQDLDLNRDDEISETEFVEGFTK
          KIAI.RLFEEIDVN..N.ISRSE..K.VK.I.FG..V....EAV.KLVQDLDLNRD.EISETEFV.G.TK
Retrocopy KIAI*RLFEEIDVNGYNQISRSEFAKLVKCIEFGQVVDDAQEAVIKLVQDLDLNRDNEISETEFVDGLTK

Parental  WMNSNSSQAANSKSSSHEIRRTWEDVE-KVIEENQTKVTSAWLTAIGYVVLGVTILALLAEPLIASVQKF
          WMNSNS.QAANSKSSS..I..TWE..E.K..EENQ...........G...L......L.........Q.F
Retrocopy WMNSNSRQAANSKSSSQGIHQTWEGAE>KGMEENQ-RINPK*HVVLGVAILSLLAEPLIVSKNSLKKQEF

Parental  SEEAGISSFFISFI
          S......SFF..FI
Retrocopy S--SFFISFFLVFI

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_38 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	GLYMA12G35670	1 retrocopy	retro_gmax_38 ,