RetrogeneDB ID: retro_oruf_34

Retrocopy location

• Organism: Brownbeard rice (Oryza rufipogon)
• Coordinates: 10:338533..340240(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ORUFI10G00220
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ORUFI07G02180
• Aliases: None
• Description: None

Sequence

>retro_oruf_34
ATGGCAGCCTCGCCGGAGTCGTCTCCGTCGTCGGCCAACTCCACCACCCCGTCAGCACCGTCGCCGTCTTCGTCGTTGTC
AAAATCACCCTCACCTCCCTCCCCATCATCGCCGCCGCCACCAGCATCGACGAACGCGCCACCAAAATCAGCTGGCGGCG
TTTCATCTTCCACGCAAGCGCAACCATCGTCGGAATCATCGTCGGAGTCTACGACTACGCCTTCGGCGCCAGCGGAGAGG
AAGAGCGGCGGGTCCTCTCGAGGAGAGTCCGGGCGGTATCGCGGTGATGTGACCGCCGGCGTGTTTGTGGGGTTATTTGT
GGTGGCGATGGTTGCGGTGTTGGCGGGTGTGGTGGCCATCGTGGTGTGCTGCTGTATAAAGATAACGAAGAAGAAGAAGC
GGCCGCCGCCGCCGAACATGCCCTTCTTCACCGACGAGAAGGGCAACGTGTACTACGCCACAGGCGGCCTGCCTCCCATG
TGGCAGCAGCACGGCAGCAGCAACTACAGCATCCCACCTCCGCCGCCGCCCGGCTGGCACATGTCATCGTCGGCGGGGGG
TTTCAGCGGCGAGATGGGGATGGGGTACTCGTCGGGACCGTACGGTCCGGCGCTGCCGCCGCCGTCGCCGAACGTGGCGC
TGGGTTTCTCCAAGAGCTCCTTCTCGTACGAGGAGCTGGCGGCGGCGACGTCGGGGTTCTCGGCGGCGAACCTGCTGGGG
CAGGGAGGGTTCGGGTACGTGTACAAGGGGGTGCTCGCCGGGAACGGGAAGGAGGTGGCGGTGAAGCAGCTCAAGTCCGG
GAGCGGGCAGGGGGAGCGGGAGTTCCAGGCGGAGGTGGACATCATCAGCCGCGTCCACCACCGCCACCTCGTGTCTCTGG
TGGGATACTGCATCGCCGCCAACCAGCGCATGCTCGTCTACGAGTTCGTCCCCAACGGCACCCTCGAGCACCACCTCTAT
AGAGGCGGCAATGGCGATCGAGTTCTAGACTGGTCGGCGCGGCACAGGATCGCGCTGGGGTCGGCCAAGGGTCTCGCCTA
CCTCCACGAAGACTGCCACCCGCGGATCATCCACCGCGACATCAAGGCGGCCAACATCCTCCTGGACGCCAACTACGAGG
CCATGGTCGCCGACTTCGGCCTCGCCAAGCTCACCACCGACACCAACACCCACGTCTCCACCCGCGTCATGGGCACCTTC
GGCTACCTGGCCCCCGAGTACGCCTCCACCGGCAAGCTCACCGAGAAGTCCGACGTCTTCTCCTTCGGCGTCATGCTGCT
GGAGCTCCTCACCGGGCGGCGGCCCGTCGACACCTCCAACTACATGGAGGACAGCCTCGTGGACTGGGCGAGGCCGGTGC
TGGCGCGCTTGCTGGTCGCCGGCGGCGAGGAAGGAGGATTAATCCGGGAGCTGGTGGACTCGCGGCTGGGCGGGGAGTAC
TCGGCGGTGGAGGTGGAGAGGATGGCGGCGTGCGCGGCGGCGAGCATCCGGCACTCGGCGCGGCAGCGGCCCAAGATGAG
CCAGATCGTGAGGGCGCTGGAGGGGGACGCCTCGCTCTCGCTGGACCACCACCACGACGACGACTTCTCCGCCTCATCGG
AGATCTCGCGGCATCGGCAGGTGGCCTTCGACAGCGGCGACTACACCGACGACTACTCCACCACCTCCACCTCCACCCAC
TCCTCCCGCCTCCCACCCAAGCGCTAA

Alignment

ORF - retro_oruf_34 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.94 %
• Parental protein coverage: 60.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PLVPPPPPPVPAGLDENAFGYDELAAATGGFSEGNMLGQGGFGYVYRGVL-GDGKEVAVKQLSAGGGQGE
          P..PPP.P.V..G.....F.Y.ELAAAT.GFS..N.LGQGGFGYVY.GVL.G.GKEVAVKQL..G.GQGE
Retrocopy PALPPPSPNVALGFSKSSFSYEELAAATSGFSAANLLGQGGFGYVYKGVLAGNGKEVAVKQLKSGSGQGE

Parental  REFQAEVDMISRVHHRHLVPLVGYCIAGAQRLLVYDFVPNRTLEHHLHK--KGLPVMKWTTRLRIAVGSA
          REFQAEVD.ISRVHHRHLV.LVGYCIA..QR.LVY.FVPN.TLEHHL.....G..V..W..R.RIA.GSA
Retrocopy REFQAEVDIISRVHHRHLVSLVGYCIAANQRMLVYEFVPNGTLEHHLYRGGNGDRVLDWSARHRIALGSA

Parental  KGLAYLHEECNPRIIHRDIKSANILLDNNFEPLVADFGMAKLTSENVTHVSTRVMGTFGYLAPEYASSGK
          KGLAYLHE.C.PRIIHRDIK.ANILLD.N.E..VADFG.AKLT....THVSTRVMGTFGYLAPEYAS.GK
Retrocopy KGLAYLHEDCHPRIIHRDIKAANILLDANYEAMVADFGLAKLTTDTNTHVSTRVMGTFGYLAPEYASTGK

Parental  LTDKSDVFSYGVMLLELLTGRRPADRSSYGADCLVDWARQALPRAMAAGG--GGGYDDIVDPRLRGEYDR
          LT.KSDVFS.GVMLLELLTGRRP.D.S.Y..D.LVDWAR..L.R...AGG..GG.....VD.RL.GEY..
Retrocopy LTEKSDVFSFGVMLLELLTGRRPVDTSNYMEDSLVDWARPVLARLLVAGGEEGGLIRELVDSRLGGEYSA

Parental  AEAARVAACAVACVRHAGRRRPKMSQVVKVLEGDVS
          .E..R.AACA.A..RH..R.RPKMSQ.V..LEGD.S
Retrocopy VEVERMAACAAASIRHSARQRPKMSQIVRALEGDAS

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Oryza rufipogon was not studied using ChIP-Seq data.

EST

Oryza rufipogon was not studied using EST data.

TSS

Oryza rufipogon was not studied using FANTOM5 data.

Lab

retro_oruf_34 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza rufipogon 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza glumaepatula	OGLUM07G14400	1 retrocopy	retro_oglu_23,
Oryza glaberrima	ORGLA07G0020300	1 retrocopy	retro_ogla_16,
Oryza rufipogon	ORUFI07G02180	1 retrocopy	retro_oruf_34 ,