RetrogeneDB ID: retro_oind_27

Retrocopy location

• Organism: Rice subsp. indica (Oryza sativa indica)
• Coordinates: 10:12999039..13001442(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BGIOSGA031915
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BGIOSGA014399
• Aliases: None
• Description: None

Sequence

>retro_oind_27
ATGGTCAGCGTCGTCCGCGCCGCGCGGCGCCAGGAGGTGTCCATATTCGACGTCGTCGTCGGCGACGTGGTGGTGCTCAA
GATCGGCGACGTCGTCCCCGCCGACGGCGTGTTCCTGGACGGCCACGCGCTGCAGGTCGACGAGTCGAGCATGACAGGCG
AGCCGCACCCCGTCGAGGTCGACGCCGTCAAGAGCCCCTTCCTCGCCTCCGGCGTCAAGGTGGTCGACGGCTACGGCAAG
ATGGTGGTCACCGCCGTCGGGACGGACACGGCGTGGGGCGAGATGATGCGCACCATCACCAGGGAGAACACCGACCCGAC
GCCGCTCCAGGAGCGCCTCGAGGGGCTCACCTCCAGCATCGGCAAGGTCGGCATCGCCGTCGCGGTGCTCGTCTTCGCCG
TGCTCACGGCGAGGCACTTCACCGGCAGCACCAGGGACGAGCAGGGCAACGCGCTGTTCGACAAGAGGAATGTCACCTTC
AACGCCGTGTTCAGCGGCCTCGTCGGCATCTTCCAGCAAGCCGTCACCATCATCGTCGTCGCCATCCCCGAGGGCCTCCC
GCTCGCCGTGACATTGACGCTGGCCTTCTCCATGAAGAGGATGGTGAGGGAGAACGCGCTGGTGCGGCGGCTGTCGGCGT
GCGAGACGATGGGCTCGGTCACCGCCATCTGCACCGACAAGACCGGGACGCTGACGCTGAACCAGATGAAGGTGACGGAG
TTCTGGGTCGGCGCCGACCGGCCAAGATCCGCCGCGGCGGTGAACGGCGGCGTCGTGAGGTTGCTCTGCCAGGGCGCCGG
GCTGAACACCACGGGCAGCGTGTACAAGCCGGACAACGTGTCGCCGCCGGAGATCACCGGCAGCCCGACGGAGAAGGCGC
TGCTGTCGTGGGCGGTGGAGGAGCTCGCCATGGACGCCGACGCGCTCAAGAGGAAATGCAAGGTGGTGCGCGTCGAGGCG
TTCAACTCCGACAAGAAGCGCAGCGGCGTGATGCTCCGCGACGCCGCCACCGGCGCGGTGACCGCGCACTGGAAAGGCGC
CGCCGAGATGGTGCTCGCGAGGTGCACCGTGTACGTCGGCGCAGACGGCGCCGCGCGCGAGCTCGGCGTGGAACAGAGGA
GGAAGCTCGAGCAGGTGATCAACGACATGGCGGCGGCGAGCCTCCGCTGCATCGCGTTCGCCTACAAGCAAGTCGTCGAC
GGCGGCGACAGCGACAACGCCAAGATCGACGACGAGGGGCTGACATTGCTGGGCTTCGTCGGACTGAAAGACCCGTGCAG
ACCAGAGGTAAAATCCGCCATCGAAGCTTGCACCAAAGCAGGCATCGCCGTCAAGATGGTCACCGGCGACAACGTCCTCA
CGGCTCGCGCCATCGCCAAGGAATGCGGCATCATCTCCGGCAACGACGACGACGCCGCCGGCGTCGTGATCGAGGGGCAC
GAGTTCCGCGCCATGTCGGAGCAGGAGCAGCTCGCCATCGTCGACAACATCCGCGTCATGGCGCGGTCGCTGCCACTCGA
CAAGCTGGTGCTCGTCCAGCGCCTGAAGCAGAAGGGCCACGTGGTGGCCGTCACCGGCGACGGCACGAACGACGCGCCGG
CGCTGAAAGAAGCCGACGTGGGCCTCTCCATGGGAGTCCAGGGCACCGAGGTCGCCAAGGAGAGCTCCGACATCGTCATC
CTCAACGACAACTTCGACACGGTGGTGACGGCGACGCGGTGGGGCCGCTGCGTGTACAACAACATCCAGAAGTTCATCCA
GTTCCAGCTCACCGTCAACGTCGCGGCGCTCGTCATCAACTTCGTGTCGGCGGTGACCACGGGCAGGATGCCGCTGACCA
CGGTGCAGCTGCTGTGGGTGAACCTGATCATGGACACCATGGGCGCGCTGGCGCTCGCCACGGACACGCCGACCAAGGGG
CTGATGCGCCGCCCGCCCATCGGCCGCACCGCGCCGCTGATCAGCAACGCCATGTGGCGCAACCTGGCGGCGCAGGCGGC
GTACCAGGTGGCCGTGCTGCTGGCGCTCCAGTACCGCGGCTTCGGCGGCGCCGGCGCCGGCGAGAGGGCGAACGGGACGA
TGATCTTCAACGCGTTCGTGCTGTGCCAGGTGTTCAACGAGTTCAACGCGAGGGAGATCGAGAGGAGGAACGTGTTCGCC
GGCGTGCACCGGAACAGGATGTTCCTGGGCATCGTCGCCGTCACGGTGGCGCTGCAGGTGGTGATGGTGGAGTTGCTGAC
CAAGTTCGCCGGAACGGAGAGGCTGGGGTGGGGGCAGTGGGGCGCCTGCGTCGGCATCGCCGCCGTGTCGTGGCCCATCG
GGTGGGCCGTCAAGTGCATCCCGGTGCCGGAGCGGCCGTTCCACGAGATCATCACGGCGAGGAGGAGGAGAAGATCGACA
TAA

Alignment

ORF - retro_oind_27 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.54 %
• Parental protein coverage: 62.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LEVVRGGRRISVSIYDLVAGDVVPLKIGDQVPADGILISGHSLSVDESSMTGESKIVHKDQ-KSPFLMSG
          ..VVR..RR..VSI.D.V.GDVV.LKIGD.VPADG....GH.L.VDESSMTGE...V..D..KSPFL.SG
Retrocopy VSVVRAARRQEVSIFDVVVGDVVVLKIGDVVPADGVFLDGHALQVDESSMTGEPHPVEVDAVKSPFLASG

Parental  CKVADGYGTMLVTAVGINTEWGLLMASISEDSGEETPLQVRLNGVATFIGMVGLSVALAVLVVLLARYFT
          .KV.DGYG.M.VTAVG..T.WG..M..I.......TPLQ.RL.G....IG.VG..VA..V..VL.AR.FT
Retrocopy VKVVDGYGKMVVTAVGTDTAWGEMMRTITRENTDPTPLQERLEGLTSSIGKVGIAVAVLVFAVLTARHFT

Parental  GHTYNPDGSVQYVKGKMGVGQTIRGIVGIFTVAVTIVVVAVPEGLPLAVTLTLAFSMRKMMRDKALVRRL
          G.T....G.....K..........G.VGIF..AVTI.VVA.PEGLPLAVTLTLAFSM..M.R..ALVRRL
Retrocopy GSTRDEQGNALFDKRNVTFNAVFSGLVGIFQQAVTIIVVAIPEGLPLAVTLTLAFSMKRMVRENALVRRL

Parental  SACETMGSATTICSDKTGTLTLNQMTVVEAYFGGKKMDPPDNVQVLSASISSLIVEGIAQNTSGSIFEPE
          SACETMGS.T.IC.DKTGTLTLNQM.V.E...G....D.P............L...G...NT.GS...P.
Retrocopy SACETMGSVTAICTDKTGTLTLNQMKVTEFWVGA---DRPRSAAAVNGGVVRLLCQGAGLNTTGSVYKPD

Parental  NGQDPEVTGSPTEKAILSWGLK-LGMRFNDTRTKSSILHVFPFNSEKKRGGVAVHLGGSESEVHIHWKGA
          N...PE.TGSPTEKA.LSW....L.M.......K.....V..FNS.KKR.GV..........V..HWKGA
Retrocopy NVSPPEITGSPTEKALLSWAVEELAMDADALKRKCKVVRVEAFNSDKKRSGVMLR-DAATGAVTAHWKGA

Parental  AEIILDSCKSWLAADGSKHSMTPEKISEFKKFIEDMAASSLRCVAFAYRTYEMVDVPSEDRRADWILPED
          AE..L..C.....ADG.......E........I.DMAA.SLRC.AFAY.....VD....D..........
Retrocopy AEMVLARCTVYVGADGAARELGVEQRRKLEQVINDMAAASLRCIAFAYK--QVVDGGDSDNAK---IDDE

Parental  DLIMLGIVGIKDPCRPGVKDSVRLCAAAGIKVRMVTGDNLQTARAIALECGILS-DPNVSEPVIIEGKAF
          .L..LG.VG.KDPCRP.VK.....C..AGI.V.MVTGDN..TARAIA.ECGI.S........V.IEG..F
Retrocopy GLTLLGFVGLKDPCRPEVKSAIEACTKAGIAVKMVTGDNVLTARAIAKECGIISGNDDDAAGVVIEGHEF

Parental  RALSDLEREEAAEKISVMGRSSPNDKLLLVKALRKRGHVVAVTGDGTNDAPALHEADIGLSMGIQGTEVA
          RA.S..E.......I.VM.RS.P.DKL.LV..L...GHVVAVTGDGTNDAPAL.EAD.GLSMG.QGTEVA
Retrocopy RAMSEQEQLAIVDNIRVMARSLPLDKLVLVQRLKQKGHVVAVTGDGTNDAPALKEADVGLSMGVQGTEVA

Parental  KESSDIIILDDNFASVVRVVRWGRSVYANIQKFIQFQLTVNVAALIINVVAAVSSGNVPLNAVQLLWVNL
          KESSDI.IL.DNF..VV...RWGR.VY.NIQKFIQFQLTVNVAAL.IN.V.AV..G..PL..VQLLWVNL
Retrocopy KESSDIVILNDNFDTVVTATRWGRCVYNNIQKFIQFQLTVNVAALVINFVSAVTTGRMPLTTVQLLWVNL

Parental  IMDTLGALALATEPPTDHLMQRPPVGRREPLITNVMWRNLIIMALFQVIVLLTLNFRG
          IMDT.GALALAT..PT..LM.RPP.GR..PLI.N.MWRNL...A..QV.VLL.L..RG
Retrocopy IMDTMGALALATDTPTKGLMRRPPIGRTAPLISNAMWRNLAAQAAYQVAVLLALQYRG

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Oryza sativa indica was not studied using RNA-Seq expression data.

ChIP-Seq

Oryza sativa indica was not studied using ChIP-Seq data.

EST

Oryza sativa indica was not studied using EST data.

TSS

Oryza sativa indica was not studied using FANTOM5 data.

Lab

retro_oind_27 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza sativa indica 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
Oryza sativa indica	BGIOSGA014399	1 retrocopy	retro_oind_27 ,
Medicago truncatula	MTR_4g008170	1 retrocopy	retro_mtru_45,