RetrogeneDB ID: retro_gmax_5

Retrocopy location

• Organism: Soybean (Glycine max)
• Coordinates: 8:3563174..3566108(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: GLYMA08G04980
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: GLYMA11G10830
• Aliases: None
• Description: None

Sequence

>retro_gmax_5
ATGACATGCAAGAAGAGGTGGCGAATGGCTTTGAATGCCATCTCTTTCGTCAAGACTCTTCACCATCTCTCCAACAAAGC
TTTTCACATCAATACCCCAACCCAGCTCTTGCGCTCCTTCTCGTACCTTTCCATTGGCGTTGCTCCAGAAGAACCCTCCT
TCAACAACGTTGATCCCAAACTTCTCAGCGATATGGTGAGGGAAAAAAGCAGCGAGTCTCTCACCCAACTTGGAGGCGTC
AAAGAACTCGCCAAACTTCTTGAAACCGACGTGAAGCGTGGCATCAGAGACATTGATAACCGAAAACGTGTCTTCGGTGA
AAACACGTTCACGAAACCTCCATCCAAAGGTTTTCTTTCTTTTGTCCTAGAATCTTTTAAAGATCCCACTATCATTATTC
TTTTGGTTTGCGCTGTTCTTTCACTTGGCTTCGGCATCAAGCAACATGGCTGGAAGGATGGATGGTACGATGGAGGAAGC
ATCATACTGGCGGTTGTTCTCGTCATTGTTGTCTCTTCCGTCAGCAACTTCAACCAATCTAGACAATTCCAGAAGCTTTC
AGCGAAAAGTGACAACTTAGGAGTGGAAGTGGTACGAGGTGGTAGACGCCAAAGGGTGTCAATCTTTGAGGTGGTGGTCG
GTGACGTTGCTTACTTGAAGATCGGTGATCAGGTTCCAGCAGATGGGGTGTTTTTAGAGGGTCATTCGTTGAAGGTGGAC
GAGTCTAGCATGACGGGGGAGAGTGACCACGTGCATGTGAACGGTGACACGAACCCTTTCTTGTTATCTGGCACAAAGGT
CACTGATGGTTTTGCACACATGCTTGTTACTTGTGTGGGTATGAACACTGCATGGGGTGCCATGATGGGTTCCATAACGA
GAGAGGTCAATGAGGAGACACCTTTGCAGGTGCGTCTCAACAAATTGACTTCTGCTATTGGCAAGGTTGGTTTGTTTGTG
GCTGCAATTGTTTTGGTGGTGTCTATGATACGGTACTTGACGGGAAGTACCAGAGATGACTTTGGGATCCGAGAATTTGT
TCGGGGAAAGACTAAGTCTGAGGATGTCATGAATGCGGTTGTGGGGATTGTTGCTGCGGCTGTGACAATTGTGGTGGTGG
CTATTCCAGAAGGGTTGCCATTGGCTGTTACTCTGAATTTGGCTTATTCCATGAAGAAAATGATGAGGGATAATGCCATG
GTTCGGAGAATCTCTGCTTGTGAGACAATGGGGTCTGCTACAACAATCTGCACTGATAAAACAGGTACACTTACGTTGAA
TGAGATGAAGGTGACAGAGGTTTGGGTGGGGAAAAAGGAAATAGGAGGAGAAGATCGTTATTTGGCGCCAAGTTTAGTTC
AATTATTGAAACAAGGGATTGGGTTGAATACCACTGCAAGTGTTTATCAGCCGCAACAAACCTCGCTGCCTGAAATTTCG
GGCAGTCCTACTGAGAAAGCGTTGCTTTCTTGGGCGGTGGTGGATTTGGGGATGGACAATATTGATGAAGTGAAGCAGAA
TTGTGAGATAATTCATGTGGAGACGTTCAACTCTGCGAAAAAGAGAAGCGGGATTCTGATGAGGGAGAAGAGAGGGAATA
TGAATATGAATATTCATACACACTGGAAGGGAGCTGCTGAGATGATATTGGCTATGTGTTCAAATTATTATGACCATACA
GGTGAAGTCATTGTCATGGATGATGGAGAAAGGGTTCAGATTGAGAACATTGTCAAGGGCATGGCAACCAAAAGTTTGAG
ATGCATTGCCTTTGCTCAAAAGAGCTGTGAAAAGCTTGAAGAGACGGGACTAACGTTGTTGGGGATACTTGGGTTGAAAG
ACCCTTGTAGGCCAGGAGTTGAAGCAGCAGTTGATTCCTGCAAGAATGCTGGAGTGAAGATCAAGATGATCACAGGAGAT
AATGTGCACACAGCAAGGGCCATAGCCTCTGAATGTGGGATTCTTTACCCTAATAATGATGAATTGGATGAAGAGGCAGT
GGTTGAAGGGTTTCAATTCAGAAACTTCTCACACGAGGAGAGAATGGATAAGATTGACAGAATCAGAGTCATGGCTAGAT
CGTCTCCATTTGACAAGCTTCTGATGGTTCAATGCTTAAAGCAGAAGGGTCATGTGGTGGCAGTCACAGGTGATGGCACA
AATGATGCACCTGCTCTCAAGGAAGCAGATATTGGACTTTCCATGGGAATACAAGGAACTGAAGTGGCAAAGGAGAGTTC
AGATATTGTTATACTTGACGACAATTTCTCTTCTGTGGTTACCGTACTAAGGTGGGGAAGATGTGTGTACACAAACATAC
AAAAGTTCATTCAGTTTCAGCTCACGGTTAACGTTGCTGCACTTGTCATCAACTTTGTAGCTGCTGTTTCTTCTGGCAAA
GTGCCTCTTTCAGCTGTCCAGCTTTTGTGGGTAAACCTGATAATGGACACTCTTGGAGCTTTGGCCTTGGCCACCGAGGA
ACCCACTAATGATCTCTTGAAGATGCCACCTGTAGGAAGAGTTGAGCCACTTATAACTAGAGTTATGTGGAGGAACCTCA
TTTCACAGGCATTGTATCAAGTGCTTGTCTTGCTGATCTTACAATTCAAGGGAAGATCAATCTTTGACGTCAGTGAGAAG
GTGAAGAACACCCTTATTTTCAATGCCTTTGTCCTCTGCCAAGTCTTCAATGAGTTCAATGCAAGGAAGCTGGAGAAGAA
GAACATCTTTGAGGGGCTTGGTAAAAATAAGTTGTTCGTGGCAATTGTGGGCCTAACTGTAATTCTTCAACTAGTGATGG
TTGAGTTTTTGAAGAAGTTTGCCAATACTGAGAGGTTGACTTGGGAGCAATGGGGTGTTTGTGTTGGCATTGGAGCTTTG
TCTTGGCCAATTGGTTTGCTGGTGAAGTGTATCTCAGTTGGTCCCAACAAGTAG

Alignment

ORF - retro_gmax_5 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.98 %
• Parental protein coverage: 94.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DIDHRKRVFGVNMLTKPPSKCFLSFVLESFNDTTIIILLVCSLLSLFFGIKQHGWKEGWYDGGSIILAVI
          DID.RKRVFG.N..TKPPSK.FLSFVLESF.D.TIIILLVC..LSL.FGIKQHGWK.GWYDGGSIILAV.
Retrocopy DIDNRKRVFGENTFTKPPSKGFLSFVLESFKDPTIIILLVCAVLSLGFGIKQHGWKDGWYDGGSIILAVV

Parental  LVIAVSSVSNFNQSKQFQKLSAKSNNMGGVEVVRGGRRQSISTFDVVVGDIVCLKVGDQVPADGVFLEGH
          LVI.VSSVSNFNQS.QFQKLSAKS.N.G.VEVVRGGRRQ..S.F.VVVGD...LK.GDQVPADGVFLEGH
Retrocopy LVIVVSSVSNFNQSRQFQKLSAKSDNLG-VEVVRGGRRQRVSIFEVVVGDVAYLKIGDQVPADGVFLEGH

Parental  SLKVDESRMTGESDHVHVHANGEIEKNPFLLLSAGTKVTDGFARMLVTSVGMNTAWGTMMGFITNKEVNN
          SLKVDES.MTGESDHVHV........NPFLL...GTKVTDGFA.MLVT.VGMNTAWG.MMG.IT..EVN.
Retrocopy SLKVDESSMTGESDHVHVNG----DTNPFLL--SGTKVTDGFAHMLVTCVGMNTAWGAMMGSIT-REVN-

Parental  EETPLQVRLNKLTSAIGKVGLLVAALVLVVSMARYFAGCTRDDFGNREFVRGRTESDDVVNAVVAIVAAA
          EETPLQVRLNKLTSAIGKVGL.VAA.VLVVSM.RY..G.TRDDFG.REFVRG.T.S.DV.NAVV.IVAAA
Retrocopy EETPLQVRLNKLTSAIGKVGLFVAAIVLVVSMIRYLTGSTRDDFGIREFVRGKTKSEDVMNAVVGIVAAA

Parental  VTIVVVAIPEGLPLAVTLSLAFSMKKMMRDNAMVRRISACETMGSATTICTDKTGTLTLNEMKVTEVWVG
          VTIVVVAIPEGLPLAVTL.LA.SMKKMMRDNAMVRRISACETMGSATTICTDKTGTLTLNEMKVTEVWVG
Retrocopy VTIVVVAIPEGLPLAVTLNLAYSMKKMMRDNAMVRRISACETMGSATTICTDKTGTLTLNEMKVTEVWVG

Parental  KRKIKADQEEDLAPSLVQLLKEGIGLNTTGSVYFHPHQTSSSLPEISGSPTEKALLSWAVEDLGMGDIDE
          K..I.......LAPSLVQLLK.GIGLNTT.SVY..P.QTS..LPEISGSPTEKALLSWAV.DLGM..IDE
Retrocopy KKEI-GGEDRYLAPSLVQLLKQGIGLNTTASVY-QPQQTS--LPEISGSPTEKALLSWAVVDLGMDNIDE

Parental  VKQHCEIIHVETFNSEKKRSGILMREKRGRSNSSNNRVHTHWKGAAEMILRMCSTYYDHTGQIIIIDDEE
          VKQ.CEIIHVETFNS.KKRSGILMREKRG.....N...HTHWKGAAEMIL.MCS.YYDHTG..I..DD.E
Retrocopy VKQNCEIIHVETFNSAKKRSGILMREKRG---NMNMNIHTHWKGAAEMILAMCSNYYDHTGEVIVMDDGE

Parental  RAQIENIVECMATKSLRCIAFAQKSLLCEKLELEETELTLLGILGLKDPCRPGVGAAVESCKNAGVKIKM
          R.QIENIV..MATKSLRCIAFAQKS..CEKLE..ET.LTLLGILGLKDPCRPGV.AAV.SCKNAGVKIKM
Retrocopy RVQIENIVKGMATKSLRCIAFAQKS--CEKLE--ETGLTLLGILGLKDPCRPGVEAAVDSCKNAGVKIKM

Parental  ITGDNAHTARAIASECGILDDELDD-DQAAVVEGFQFRNFSHEERMDKIDRIKVMARSSPSDKLLMVQCL
          ITGDN.HTARAIASECGIL....D..D..AVVEGFQFRNFSHEERMDKIDRI.VMARSSP.DKLLMVQCL
Retrocopy ITGDNVHTARAIASECGILYPNNDELDEEAVVEGFQFRNFSHEERMDKIDRIRVMARSSPFDKLLMVQCL

Parental  KQKGHVVAVTGDGTNDAPALKEADIGLSMGIQGTDVAKESSDIVILDDNFSSVVTVLERGRCVYANIQKF
          KQKGHVVAVTGDGTNDAPALKEADIGLSMGIQGT.VAKESSDIVILDDNFSSVVTVL..GRCVY.NIQKF
Retrocopy KQKGHVVAVTGDGTNDAPALKEADIGLSMGIQGTEVAKESSDIVILDDNFSSVVTVLRWGRCVYTNIQKF

Parental  IQFQLTVNVAALAINFVAAVSSGKVSLSAVQLLWVNLVMDTLGALALATEQPTNDLMNMPPVGRVDPLIT
          IQFQLTVNVAAL.INFVAAVSSGKV.LSAVQLLWVNL.MDTLGALALATE.PTNDL..MPPVGRV.PLIT
Retrocopy IQFQLTVNVAALVINFVAAVSSGKVPLSAVQLLWVNLIMDTLGALALATEEPTNDLLKMPPVGRVEPLIT

Parental  RVMWRNLISQAVYQVLVLLTLQFEGRSSIFGGVNEKVKNTMIFNAFVLCQVFNEFNARKLETKNIFEGLG
          RVMWRNLISQA.YQVLVLL.LQF.GR.SIF..V.EKVKNT.IFNAFVLCQVFNEFNARKLE.KNIFEGLG
Retrocopy RVMWRNLISQALYQVLVLLILQFKGR-SIF-DVSEKVKNTLIFNAFVLCQVFNEFNARKLEKKNIFEGLG

Parental  KNKLFMVIVGLTVVLQLVMVEFLNKFANTERLTWEQWCVCVAIGVLSWPIGLLVKCLPV
          KNKLF..IVGLTV.LQLVMVEFL.KFANTERLTWEQW.VCV.IG.LSWPIGLLVKC..V
Retrocopy KNKLFVAIVGLTVILQLVMVEFLKKFANTERLTWEQWGVCVGIGALSWPIGLLVKCISV

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_5 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	GLYMA11G10830	1 retrocopy	retro_gmax_5 ,