RetrogeneDB ID: retro_gmax_14

Retrocopy location

• Organism: Soybean (Glycine max)
• Coordinates: 1:35413197..35414957(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: GLYMA03G37441
• Aliases: None
• Description: None

Sequence

>retro_gmax_14
AAGGATGTCATATTTTTGCCTTCTTTTGTGGCAATACCAGTTCGTCCAAGACCTGGTGTTTGGGAATATGTTTGTGTTAA
TGTCTCTGACCTCAGCCTGGAGCAATTAAGCATTTCTGAATATCTCAGCTTCAAGAAGAACTTGTCGATGGAAAGATTAA
TGACAATTTTGTATTGGAGCTTGACTTTGAGCCATTTAATGCCACATTTCCTTGCCCATTCCACTCCGCATCCATTGGCA
ATGGTGTCCAATTTCTTAATCGCCACCTCTCACCAATTATGTTTCGCACCAAAGATTCCTTGCAACCTTTGCTTGATTCC
CTCCAAGCTCACAAATACAAGGGTCATACTCTAATGATAAATGATAGAGTACAAACCTTTTCCAATCTTCAGTCTGCATT
AGCCATGACCAAGGATTATCTTTCTAAACTTGCTAGTGATACACTCTATTCAGAGTTTGAATATGTATTACAAGGAATGG
ATTTTGAGAGAGGTTGGGGTGATACTATTGAACAGGTATTGGAAATGATGCATCTGTTCCTGGATTTTCTTCAGGCTCCT
GATCATTATGCACTAGAGACTTTTCTTGGGAGAGAGCCAATGGTATTCAACGTTGCTATATTATCTCCTCATGGCTACTT
TGGACAAGCCAATGTCTTGGGTTTGCCTGACATTGGTGGCCAAGTTGTTTATATACTAGATCAAGTGTGTGCCCTTGAAA
ATGAGATGCTCCTTCAGATCAAGAAACAAGGGCTTGATTTCACTCCTAGAATTCTAATTTTTACCAGGTTAATAGCCAAT
GCAAAGGGGACAACATGCAACCAGCGGTTAGAAAGAGTTAGTGGTACTGACCATACTCATATTTTGCGAGTTCAATTCAG
ATCAGAGTTAGGAACTCTCAGTAAATGGAACTCAAGGTTTCTTGTGTGGACTTATCTAGAGACTTATGTAGAAGCTGTTG
CAAGTGAAATTGTTGCTGAGTTACAAGGGCATCCTACTTCTATCATTGGAAATTACAGTGATGGGAATCTTGTTGCATCT
TTATTGGCTTATAAAATGGGAGTTACTCGGTGCACAATCACACATGCACTTGAGAAGACAAAATATCTAAAGTCATATTT
ATATTGGAAGAAATTTGAGGATATATCCCACTTTTCATGCCAATTTACTTTTGACCTAATAGCCGGATATAATGTTGATT
TTACAATCACCAGTACATACCAGGAGATTACAGGAACAAAAAATACTGTCAGGCAGTATGAGAGCCACACTAGTTTTATC
TTCCCGGGCTCTATAGGGTTATCCATGGCATTGATGTTTTAATCCCAAGTTCAATATTGTCTCTCTTGGAGTTGATATGT
CAACATATTTCCCATACTCTGAAAAGCAGAACAGGCTTATAGCCCTACATAGTTCAATTGAAAAGTTGTTATTTGATCCT
GAGCAGACTAATGAATGCGTTGGTTCATTGAAAGACAAGTCAAAGCCCGTAATTTTCTCCATGGCAAGGTTAGACAAAGT
GAAAAACATAATTGGATTGGTAGAATGCTTTGGTAAGAACAACATATTGAGGGAACTGGTCAACCTTGTCGTAGTAGCTG
GTTATATTGATGTAAAGAAGTCCAATGAAAGAGCAGAAATTGCAGAAATTGAGAAGATGCACGAGCTCATGAAAAATATC
ATTTAAATGGTGATTTTCGTTGGGTTGTTGCCCAAACAAATAGGGTAGGTAACGAGGAGTTGTGTCGCTACATAGCAGAC

Alignment

ORF - retro_gmax_14 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.46 %
• Parental protein coverage: 72.41 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KEAIVLPPFVAIAVRPRPGVWEYVRVNVSDLSVEQLSISEYLSFK-EELVDGKINENFVLELDFEPFNAT
          K..I.LP.FVAI.VRPRPGVWEYV.VNVSDLS.EQLSISEYLSFK.EELVDGKIN.NFVLELDFEPFNAT
Retrocopy KDVIFLPSFVAIPVRPRPGVWEYVCVNVSDLSLEQLSISEYLSFK<EELVDGKINDNFVLELDFEPFNAT

Parental  FPRPTRSASIGNGVQFLNRHLSSIMFRNKDSLQPLLDFLRAHKYKGHALMINDRVQTISNLQSALAKTED
          FP.P..SASIGNGVQFLNRHLS.IMFR.KDSLQPLLD.L.AHKYKGH.LMINDRVQT.SNLQSALA.T.D
Retrocopy FPCPFHSASIGNGVQFLNRHLSPIMFRTKDSLQPLLDSLQAHKYKGHTLMINDRVQTFSNLQSALAMTKD

Parental  YLSKLASDTLYSEFEYVLQGMGFERGWGDTAERVLEMMHLLLDILQAPDPSTLETFLGRVPMVFNVVILS
          YLSKLASDTLYSEFEYVLQGM.FERGWGDT.E.VLEMMHL.LD.LQAPD...LETFLGR.PMVFNV.ILS
Retrocopy YLSKLASDTLYSEFEYVLQGMDFERGWGDTIEQVLEMMHLFLDFLQAPDHYALETFLGREPMVFNVAILS

Parental  PHGYFGQANVLGLPDTGGQVVYILDQVRALENEMLLRIKKQGLDFTPRILIVTRLIPDAKGTTCNQRLER
          PHGYFGQANVLGLPD.GGQVVYILDQV.ALENEMLL.IKKQGLDFTPRILI.TRLI..AKGTTCNQRLER
Retrocopy PHGYFGQANVLGLPDIGGQVVYILDQVCALENEMLLQIKKQGLDFTPRILIFTRLIANAKGTTCNQRLER

Parental  VSGTDHTHILRVPFRSESGTLRKWISRFDVWPYLETYAEDVASEIAAELQGYPDFIIGNYSDGNLVASLL
          VSGTDHTHILRV.FRSE.GTL.KW.SRF.VW.YLETY.E.VASEI.AELQG.P..IIGNYSDGNLVASLL
Retrocopy VSGTDHTHILRVQFRSELGTLSKWNSRFLVWTYLETYVEAVASEIVAELQGHPTSIIGNYSDGNLVASLL

Parental  AYKMGVTQCTIAHALEKTKYPDSDLYWKKFEDKYHFSCQFTADLIAMNNADFIITSTYQEIAGTKNTVGQ
          AYKMGVT.CTI.HALEKTKY..S.LYWKKFED..HFSCQFT.DLIA..N.DF.ITSTYQEI.GTKNTV.Q
Retrocopy AYKMGVTRCTITHALEKTKYLKSYLYWKKFEDISHFSCQFTFDLIAGYNVDFTITSTYQEITGTKNTVRQ

Parental  YESHTGFT-LPGLYRVVHGIDV-FDPKFNIVSPGADMSIYFPYSEKQNRLTALHGSIEKLLFDPEQTDEY
          YESHT.F..LPGLYRV.HGIDV.F.PKFNIVS.G.DMS.YFPYSEKQNRL.ALH.SIEKLLFDPEQT.E.
Retrocopy YESHTSFI<LPGLYRVIHGIDV<FNPKFNIVSLGVDMSTYFPYSEKQNRLIALHSSIEKLLFDPEQTNEC

Parental  IGSLKDKSKPIIFSMARLDRVKNITGLVECFGKNSKLRELVNLVVVAGYIDVKKSSDREEIAEIEKMHEL
          .GSLKDKSKP.IFSMARLD.VKNI.GLVECFGKN..LRELVNLVVVAGYIDVKKS..R.EIAEIEKMHEL
Retrocopy VGSLKDKSKPVIFSMARLDKVKNIIGLVECFGKNNILRELVNLVVVAGYIDVKKSNERAEIAEIEKMHEL

Parental  MK-KYNLNGDFRWIAAQTNRARNGELYRYIAD
          MK.KY.LNGDFRW..AQTNR..N.EL.RYIAD
Retrocopy MK<KYHLNGDFRWVVAQTNRVGNEELCRYIAD

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_14 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	GLYMA03G37441	1 retrocopy	retro_gmax_14 ,