RetrogeneDB ID: retro_oruf_4

Retrocopy location

• Organism: Brownbeard rice (Oryza rufipogon)
• Coordinates: 6:3223497..3224970(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ORUFI06G04730
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ORUFI06G04700
• Aliases: None
• Description: None

Sequence

>retro_oruf_4
ATGGCTTGTGCGAGCGCGGGAAAACGTGATATGATGAATCAGCCGGGACATGGTGGTGATCTGCCCGTGGCCAAGCGGCG
GCGGTGCGTCGAACCCACCGGCGCCGCCGCAGCCTGCATCCCGGAAGACGTCATCGAGCAAATCCTCCTCCGTCTCCCCG
TCAAGTCCATCCTGCGGTTCAGGTCCGTGTGCAAGTCGTGGCGCTCCATGGTCGCCGAGCCGCACTTCGTTCGCCTCCAG
CTGCACCACTCCACCACGGCGGCGCGCCGCCGTCCACCGTCCATGCTCGTACTGTCAGGCTGGCGTATCCTACAGGAACG
GATGGGATCGATATGCTTCTTTCGCTACCCGGGGCATGGCGCCCTCGCGGACCTCGCGTATGAGATGACATGCTCCTCGG
CCGTCGCCACCGCCGACGAGGATGATACCGCCGACTGGGACGCCGTCGACGATGGGGATGCCGTGGATGACGGGGACGAC
GCCGCGGACTGGGACACCGACGATGACGGGGACGACGCTACGGACTGGGACACCGACGATGACGGGGACGACGCTACTAC
GGATTGGGACACCGACGATGACGGGGACGGCGCCGACCGGTACATCAACAATGGCGCCATCAGGTTTGGCCTCCCTCTGC
ACTGCAACGGGCTCGTGTTGCTGAGCACGATGGAGAACTCCTCTATGATGTTAGTTTGCAACCCGGCAACGAGGGAGTTC
GCCGAGCTACCGGCCTGTACGCCGGACTACTTGAGGATCCAAAGAGTAGGCTTCTACGCCGACCAGCCTACAGGCAAGAC
GAAGGTGGTTCGCTACTTCATCCGCCACTGCAACGAAACCTACACGGACTACAGCGTCGGATGCGAGGTTTTGTCCCTCG
GCTCGCCGGCGTGGAGGCCGCTCGCCGACCCTCCCTACCTCGTCCTGAACAAAACGTCACCGTGCATCCTCGGTGGCATC
TACTGGATCGCCATCCTACCGTCGCCGCCCACCGGCAGCTGCACCACCCCCGGAAAAATGCTACGCTTCGACGTGTGCAG
CGAGGAGTTTACCAGTTTCCCGAGCCCACCGTTCATGGAGCGGCAGGAGATATGTGACGTTAATGGGACCCTGACGGAGC
TGGCCGGAAAGCTGTGCTATATGCACACTCCCGCCGACGGTAAAGTTGAGCTCTGGACAGCTTCCGCCGCCGACGAAGGG
CCGCGATGGTCGCTGCATTGCACCGTCGTGCTATCGTACCCCTTTCAAACCATCTACCCATTTGACCACGATTACCAAGG
AAGCATATTTTTCAACGCGGATTGCGCCTTGATTTACCGGTACGATGTGGAACGCGGAGTTGCGGAACGCGTGGTGGACA
TGATCGACGATATGACCTACATCAACCGTTCCAAGCTGTACCGTGGTCCAGGTTACTTGAAGTACCGTACCATTCAGTAC
AGTGAGAGCCTGGTATCCGTCCAAGCAAATTAA

Alignment

ORF - retro_oruf_4 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.86 %
• Parental protein coverage: 71.37 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AAADGYAAADWDAVDDGADAADDGAAADNLDDAVDDGDAAADWDDDDDWDDDVGAIGWGMHLHCNGLVLL
          A..DG..AADWD..DDG.DA..D....D..DDA..D.D...D.D..D......GAI..G..LHCNGLVLL
Retrocopy AVDDGDDAADWDTDDDGDDAT-DWDTDDDGDDATTDWDTDDDGDGADRYINN-GAIRFGLPLHCNGLVLL

Parental  RSTMKYSTQMLMLVCNPATKELAELPDCAPDYFGVQAVSFYADQSTGKTKVVHCFIRHCDKTYTDYSVGC
          .STM..S....MLVCNPAT.E.AELP.C.PDY...Q.V.FYADQ.TGKTKVV..FIRHC..TYTDYSVGC
Retrocopy -STMENSS--MMLVCNPATREFAELPACTPDYLRIQRVGFYADQPTGKTKVVRYFIRHCNETYTDYSVGC

Parental  EVLSLGSPAWRPVADPPYLVKTKTSPCILGGIYWIAALPSPSTGSCTTPG-VVRFDVCSEEFASFPCPPF
          EVLSLGSPAWRP.ADPPYLV..KTSPCILGGIYWIA.LPSP.TGSCTTPG...RFDVCSEEF.SFP.PPF
Retrocopy EVLSLGSPAWRPLADPPYLVLNKTSPCILGGIYWIAILPSPPTGSCTTPGKMLRFDVCSEEFTSFPSPPF

Parental  MERQKMSDVACGDLTELGGKLCYVHAPADDRVELWTASAADGGGSRPRPRWSLQCTVVLPPSFDTFFQFT
          MERQ...DV..G.LTEL.GKLCY.H.PAD..VELWTASAAD.G...PR..WSL.CTVVL...F.T...F.
Retrocopy MERQEICDVN-GTLTELAGKLCYMHTPADGKVELWTASAADEG---PR--WSLHCTVVLSYPFQTIYPFD

Parental  YDYQGGIFFYVDYAMIYRYDVERRVVERVVDMLEEMTYFDRSRRKLDRCDGDWMHYAIQYSESLVSIQAN
          .DYQG.IFF..D.A.IYRYDVER.V.ERVVDM...MTY..RS..KL.R..G......IQYSESLVS.QAN
Retrocopy HDYQGSIFFNADCALIYRYDVERGVAERVVDMIDDMTYINRS--KLYRGPGYLKYRTIQYSESLVSVQAN

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_4 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryza rufipogon	ORUFI06G04700	1 retrocopy	retro_oruf_4 ,