RetrogeneDB ID: retro_oniv_3

Retrocopy location

• Organism: Indian wild rice (Oryza nivara)
• Coordinates: 12:2819150..2820449(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ONIVA12G03540
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ONIVA11G03830
• Aliases: None
• Description: None

Sequence

>retro_oniv_3
ATGGAAGGCAACAACCTACCCTCTGGAAGCTTGATGCGTTCTAACTCTGGGCAAATGCATGCTCCAAATCCTGGAAAGCA
GGGCTTTGACCATACTCAGATGCCTGGCAATTTATCGATGTATGTAAACCAGTCTACAGATTCTGATCACTTGTCAGAAT
TTCAATTCGGAGAGCTTGGAAAGGTTGACCACCACCACCACCATCACCATCGTCAACACGCCAAGAACAGCATGAGTGAT
GATGAGGAACATGGTGTCAACGAGGATGCCACTGATAGCCAGAGCGGCAAGGGAAAGAAGGGCGCTGCATGGCAGCGGAT
GAAGTGGACTGATTCAATGGTCAAGCTTTTAATTACTGCAGTATCTTACACTGGGGAGGATCCAGGAGCTGATTCAGGAG
CTGGGAAGAGAAACTCTGCAATAATGCAGAAAAAGGGCAAGTGGAAGGCAATATCAAAGGTCATGGGTGAGCGAGGCTGC
AGTGTATCACCGCAGCAATGTGAAGATAAATTCAATGATCTCAATAAGAGATACAAAAGACTTACAGATATCCTTGGCCG
GGGTACAGCTTGCAAGATTGTGGAGAATCATGCTCTGCTGGATTGCATGAGTAATCTGTCTGACAAGATGAAAGATGATG
CGAGGAAGATACTGAGTTCAAAGCACTTGTTCTACGAGGAGATGTGCTCCTACCATAATAACAATCGAGTGAGTTTGCCT
GAAGATCCTGCCCTTCAGCGTTCACTGCAGCTTGCCCTTAGATGTAAAGATGAGCATGATCTGAGGAGGGGAACAAGCGG
AGATGCCGATGAAGATGATCAAAGTGTAGACTCTGATTCCGAGGAGGAGAATGATGAGGAAAATTACACATTACAAGGTG
ATAAGAGTGCCCTGCCCATGCATAAAAGATTGAGGCTTATGACAGATCAGGAGGATGTGGGTTTTGGCAACTCTTCCAGC
TCACATGGATGTAGCAGGAGGTCTGATTCCCATGGCATATCACTGGATATCAACAAAGCATTTCCTGATGGAACCAACTT
GGCTTTGGCGCAAAAGGATTTGGCTAAACAATCTGCAGATCTTGAGGAACAAAGGTTGCAGATTGAAGTCCAGGCAGTCT
ATCTTGCAAAACAACGGCTCAAATGGGAGCGCTTCAGTAAAAATAAGGATAGAGAACTGGAACAAATGAGGTTAGAGAAT
GAAAAAATGAGGCTTGAGAATAAGCGCTTGGAGCTGGAGGTAAGGCACAAAGAGTTAGAGCTTGAACTCAAGCAAAAAGG
CAGTGGCAATCATGCATGA

Alignment

ORF - retro_oniv_3 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.44 %
• Parental protein coverage: 92.99 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SKQMHPPNSGNQGFNQPQIPGNFTIPMDRVTEPDNISDGVQLGQHGKIAHHHHHH-RHHSKNHGSDEEEH
          S.QMH.PN.G.QGF...Q.PGN........T..D..S...Q.G..GK..HHHHHH.R.H.KN..SD.EEH
Retrocopy SGQMHAPNPGKQGFDHTQMPGNLSMYVNQSTDSDHLSE-FQFGELGKVDHHHHHHHRQHAKNSMSDDEEH

Parental  DMNEDAAD---GKDKKGSPWHRMKWTDSMVKLLITAVSYTGEDPGADLGGGRRNYSMMQKKGKWKAISKV
          ..NEDA.D...GK.KKG..W.RMKWTDSMVKLLITAVSYTGEDPGAD.G.G.RN...MQKKGKWKAISKV
Retrocopy GVNEDATDSQSGKGKKGAAWQRMKWTDSMVKLLITAVSYTGEDPGADSGAGKRNSAIMQKKGKWKAISKV

Parental  MGERGCHVSPQQCEDKFNDLNKRYKRLTDILGRGTACNVVENHSLLDHM-DISEKMKEDARKILNSKHLF
          MGERGC.VSPQQCEDKFNDLNKRYKRLTDILGRGTAC..VENH.LLD.M...S.KMK.DARKIL.SKHLF
Retrocopy MGERGCSVSPQQCEDKFNDLNKRYKRLTDILGRGTACKIVENHALLDCMSNLSDKMKDDARKILSSKHLF

Parental  YEEMCSYHNNNRISLPEDPALQQSLQLALRCKEDNDFMRHASGDAELDDDQSEDSD-YEGNEEEHRAVDT
          YEEMCSYHNNNR.SLPEDPALQ.SLQLALRCK...D..R..SGDA...DDQS.DSD..E.N.EE......
Retrocopy YEEMCSYHNNNRVSLPEDPALQRSLQLALRCKDEHDLRRGTSGDAD-EDDQSVDSDSEEENDEENYTLQG

Parental  NIRGPSMHKRMWHVVDYGDVGFVTSCSNDG-SGRSDPYDV-LDINKPFPDGCDLALVQKDLALKAAEIQK
          ......MHKR.....D..DVGF..S.S..G.S.RSD.....LDINK.FPDG..LAL.QKDLA...A....
Retrocopy DKSALPMHKRLRLMTDQEDVGFGNSSSSHGCSRRSDSHGISLDINKAFPDGTNLALAQKDLAKQSADLEE

Parental  HRLQIETKAVQLAKQRLKWEMFRKNKDLELEKLALENEQMMLQNKREFTLKLGVLFLTMNAEVKSKCGG
          .RLQIE..AV.LAKQRLKWE.F.KNKD.ELE...LENE.M.L.NKR...L.L.V.......E.K.K..G
Retrocopy QRLQIEVQAVYLAKQRLKWERFSKNKDRELEQMRLENEKMRLENKR---LELEVRHKELELELKQKGSG

Legend:

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

Expression

RNA-Seq

Oryza nivara was not studied using RNA-Seq expression data.

ChIP-Seq

Oryza nivara was not studied using ChIP-Seq data.

EST

Oryza nivara was not studied using EST data.

TSS

Oryza nivara was not studied using FANTOM5 data.

Lab

retro_oniv_3 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza nivara 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 nivara	ONIVA11G03830	1 retrocopy	retro_oniv_3 ,