RetrogeneDB ID: retro_oruf_21

Retrocopy location

• Organism: Brownbeard rice (Oryza rufipogon)
• Coordinates: 1:10143146..10144028(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ORUFI01G13460
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ORUFI05G02420
• Aliases: None
• Description: None

Sequence

>retro_oruf_21
ATGGACGCGCCGTGTGGATGGACGACGTCGGCGGCGGCGGCGGTGGCGGAGGAGGAGGATGTTCGGAGAGGGCCGTGGAC
GGTGGAGGAGGACGCGGTGCTGGCCGGGTACGTGGCGGCGAACGGCGAGGGGCGGTGGAACGAGCTGGCGCGGGCGGCGG
GGCTGAGGCGCACGGGGAAGAGCTGCCGCCTCCGGTGGCTCAACTACCTCCGCCCCGACGTGCGCCGCGGCGACTTCACC
CCGCAGGAGCAGCTGCTCATCCTCGAGCTCCACTTCCGGTGGGGGAACCGCTGGTCCAGGATCGCGCAGCACATGCCGGG
GAGGACGGACAACGAGATCAAGAACTACTGGCGGACCAGGGTGCAGAAGCACGCCAAGCAGCTCGGCTGCGACGTCAATA
GCCGCCAGTTCAAGGACGTCATGAGGCACCTCTGGATGCCGCGCCTCGTCGAGAGGATCCACGCCGCCGCCGCCTCGTCG
GAACGCGCCGCGCCGCCGCCGTGTGCCGCCGCGCCGGCTAGTCACAGCGGCATGTGCCACTCACCTGACCCGTCAACCAC
GACGTCGAGCACGGCAGGGTCGTCGGTGACGCACGGCGAGCAGTTCCCGTCGTCGACGAACCACCACCTGATGACCATGG
CCAGCGTCACCACCGCAGCGGCAGATTGGTCCAGCGAGCAATGCGGCAGCGGCAGCGCCACCAGCACGAGCGTTGGGATC
AGTTATGACATGTTCGAGGGGAGCTGGTCGGAGCTCCTCGCCCGCGCCTACGACGACGACGGCGCCGATTCTTCGCTGCT
GCCGGACTTCCAAATGGCAGACACCGGAGACAACTGCTGGTGGAGTAATTTGGAGGACATCTGGTCACAGCAGCCGTACT
GA

Alignment

ORF - retro_oruf_21 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.12 %
• Parental protein coverage: 54.14 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SPAMSSATAAAASEDEGDLRRGPWTVEEDMLLVDYIANHGEGRWNSLARCAGLRRTGKSCRLRWLNYLRP
          .P......AAAA...E.D.RRGPWTVEED..L..Y.A..GEGRWN.LAR.AGLRRTGKSCRLRWLNYLRP
Retrocopy APCGWTTSAAAAVAEEEDVRRGPWTVEEDAVLAGYVAANGEGRWNELARAAGLRRTGKSCRLRWLNYLRP

Parental  DVRRGNITADEQLLILDLHSRWGNRWSKIAQYLPGRTDNEIKNYWRTRVQKHAKQLRCDVNSKEFRDVVR
          DVRRG..T..EQLLIL.LH.RWGNRWS.IAQ..PGRTDNEIKNYWRTRVQKHAKQL.CDVNS..F.DV.R
Retrocopy DVRRGDFTPQEQLLILELHFRWGNRWSRIAQHMPGRTDNEIKNYWRTRVQKHAKQLGCDVNSRQFKDVMR

Parental  HVWMPRLVERIQADAAAAGEVAAPAPVSAA
          H.WMPRLVERI.A.AAA..E.AAP.P..AA
Retrocopy HLWMPRLVERIHA-AAASSERAAPPPCAAA

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_21 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza brachyantha	OB05G12230	1 retrocopy	retro_obra_10,
Oryza glumaepatula	OGLUM05G02350	1 retrocopy	retro_oglu_19,
Oryza nivara	ONIVA05G02220	1 retrocopy	retro_oniv_30,
Oryza punctata	OPUNC05G02190	1 retrocopy	retro_opun_37,
Oryza glaberrima	ORGLA05G0022200	1 retrocopy	retro_ogla_43,
Oryza rufipogon	ORUFI05G02420	1 retrocopy	retro_oruf_21 ,