RetrogeneDB ID: retro_oind_51

Retrocopy location

• Organism: Rice subsp. indica (Oryza sativa indica)
• Coordinates: 1:26129090..26130368(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BGIOSGA003912
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BGIOSGA016543
• Aliases: None
• Description: None

Sequence

>retro_oind_51
ATGGCAGATCAGAAGGTGATTCTCGCCGAGCCGCTGCTTCCGGGGAAGGAAGCTGACTTCGCCGACGACGACGACGACGT
GGAGGCGCAGCTCACTTCGTACCACACCGGCGCCTCCTTCTCCAGGACGTGCCTCAACCTCACCAATGCCGTCTCCGGCA
TCGGGGTGCTGTCCATGCCGTACGCGGTGTCGCAGGGCGGGTGGCTCAGCCTGCTGCTCTTCGTCCTTGTCGGCGCCGTC
TGCTACTACACCGGCACGCTCATCGAGCGCTGCATGCGCGCCGACGGCTCCATCGCCAGCTACCCAGACATCGGCCAGTT
CGCCTTTGGCGCCGCCGGCCGGAGAGCCGTCGCCTTCTTCATGTACGTCGAGCTCTACCTCGTCGCCATAAGCTTCCTCG
TCCTCGAGGGCGACAATCTCGACAAGCTCTTCCCCGGCGCAACCATGGAGATTCTTGGCTACCAGCTCCACGGCAAGCAG
CTATTCATTGTCCTCGCCGCCGCCGTCATACTGCCCACTACCTGGCTCAAGAATCTTGGCATGCTCGCTTACGTGTCAGC
GGCCGGGCTCATCGCCTCGGTGGCCTTGACAGCGTCACTGATCTGGGCCGGTGTCGCCGAGACCGGGTTCCACCGGAACA
GCAACACACTCAACCTCGCCGGAATCCCCACCTCCCTCGGTCTCTACTTTGTCTGCTTCACCGGCCACGCCGTCTTCCCG
ACGATATACTCCTCCATGAAGAACAGCAAACACTTCTCCAAAGTTCTCTTGATCTCATCGGTGCTGTGCAGCCTCAACTA
CGGGCTCACGGCGGTGCTGGGCTACCTGATCTACGGTGACGATGTGCAGTCGCAGGTGACGCTGAACCTGCCCTCCGGCA
AGCTCTACACCAAGATCGCCATCGTGATGACGCTGGTGAACCCGATGGCCAAGTACGCGCTGCTCGTGGCGCCGATCACG
GCGGCCGTCGAGGAGAGGCTGTCTCTGACGCGAGGCAGCGTGCCGGTGAGGGTGGCCATCAGCACCGCCATCCTCGCCAG
CACGGTGGTGGTGGCGTCGACGGTGCCTTTCTTCGGCTACCTCATGTCATTCATCGGCTCGTTCCTCAGCGTCATGGCGA
CCGTGTTGTTCCCTTGCCTCTGCTACCTCAAGATCTACAAGGCCGATGGCATCCGCCACACGGAGATGGTGGCCATCGCC
GGAATTCTGCTGCTAGGAGTGTTCGTCGCCGTCACCGGCACGTACACTTCTTTGCTGCAGATTATAGCCACTTTCTGA

Alignment

ORF - retro_oind_51 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.71 %
• Parental protein coverage: 93.19 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EQPLLQAHAAVPARGKQEPVERDHEAQCSPEADGDGATFVRTCFNGLNALSGVGLLSIPYALSEGGWLSL
          .Q....A....P..........D............GA.F.RTC.N..NA.SG.G.LS.PYA.S.GGWLSL
Retrocopy DQKVILAEPLLPGK-EADFADDDDDVEAQLTSYHTGASFSRTCLNLTNAVSGIGVLSMPYAVSQGGWLSL

Parental  VLLLAVAMVCCYTGLLLRRCMAASPAVRGYPDIGALAFGAKGRLAVSAFLYAELYLVAIGFLILEGDNLD
          .L...V..VC.YTG.L..RCM.A......YPDIG..AFGA.GR.AV..F.Y.ELYLVAI.FL.LEGDNLD
Retrocopy LLFVLVGAVCYYTGTLIERCMRADGSIASYPDIGQFAFGAAGRRAVAFFMYVELYLVAISFLVLEGDNLD

Parental  KLFPGTSLAVGGLVVSGKQLFVVVVAVVILPTTWLRSLAVLAYVSASGVLASVVVVFCVLWAAVFDGVGF
          KLFPG......G....GKQLF.V..A.VILPTTWL..L..LAYVSA.G..ASV.......WA.V....GF
Retrocopy KLFPGATMEILGYQLHGKQLFIVLAAAVILPTTWLKNLGMLAYVSAAGLIASVALTASLIWAGVAE-TGF

Parental  HGKGRMLNVSGLPTALGLYTFCYCGHAIFPTLCNSMQEKDKFSRVLVICFVACTVNYGSMAILGYLMYGD
          H.....LN..G.PT.LGLY..C..GHA.FPT...SM.....FS.VL.I..V.C..NYG..A.LGYL.YGD
Retrocopy HRNSNTLNLAGIPTSLGLYFVCFTGHAVFPTIYSSMKNSKHFSKVLLISSVLCSLNYGLTAVLGYLIYGD

Parental  DVKSQVTLNLPEGKISSKLAIYTTLINPFSKYALMVTPVATAIEEKL-LAGNKRSVNVLIRTLIVVSTVV
          DV.SQVTLNLP.GK...K.AI..TL.NP..KYAL.V.P...A.EE.L.L......V.V.I.T.I..STVV
Retrocopy DVQSQVTLNLPSGKLYTKIAIVMTLVNPMAKYALLVAPITAAVEERLSLTRGSVPVRVAISTAILASTVV

Parental  IALTVPFFGHLMALVGSLLSVMASMLLPCICYLKIFGLTRCGRGETLLIAAIIVLGSLVAATGTYSSLKK
          .A.TVPFFG.LM...GS.LSVMA..L.PC.CYLKI.........E...IA.I..LG..VA.TGTY.SL..
Retrocopy VASTVPFFGYLMSFIGSFLSVMATVLFPCLCYLKIYKADGIRHTEMVAIAGILLLGVFVAVTGTYTSLLQ

Parental  IFYEF
          I...F
Retrocopy IIATF

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_51 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA016543	1 retrocopy	retro_oind_51 ,