RetrogeneDB ID: retro_opun_37

Retrocopy location

• Organism: Red rice (Oryza punctata)
• Coordinates: 1:10817746..10818625(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OPUNC01G12250
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OPUNC05G02190
• Aliases: None
• Description: None

Sequence

>retro_opun_37
ATGGACGCGCCGTGTGGATGGACGTCTGCGGCGGCGGCGGCGGTGGCGGTGGCGGAGGAGGAGGATCTTCGGAGAGGGCC
GTGGACAGTGGAGGAGGACGCGGTGCTGGCCGGGTACGTGGCGGCGAACGGCGAGGGGCGGTGGAACGAACTGGCGCGCG
CGGCGGGGCTGAGGCGCACGGGGAAGAGCTGCCGCCTCCGGTGGCTCAACTACCTCCGCCCCGACGTGCGCCGCGGCGAC
TTCAACCCGCAGGAGCAGCTGCTCATCCTCGAGCTCCACTTCCGGTGGGGGAACCGCTGGTCCAAGATCGCGCAGCACAT
GCCCGGGAGGACGGACAACGAGATCAAGAACTACTGGCGGACCAGGGTGCAGAAGCACGCCAAGCAGCTCGGCTGCGACG
TCAACAGCCGCCAGTTCAAGGACATCATGAGGCACCTCTGGATGCCGCGCCTCGTCGAGAGGATCCAGGCCGCCGCCTCG
TCGGAACGCGCCGCGCCGCCGTGTGCCGTGCCGGTTCACAGCGACATGTGCCACTCACCTGACCCGTCAACGACGACGAC
GACGTCGAGCACGGCAGGGTCATCGTCGATAACGTCCACGTCGGTGCCGCACGACGAGCAGTTCTCGTCGTCGACGAACC
GCCACCTGACCACGGCCAGCGTCACCACCGCAGCAGCGCCAGATTGGTCCAGCGAGCAATGCGGCAGCGCGAGCGCCGGG
ATCAGTGATGACATGTTCGAGGGGAGCTGGTCGGAGCTCCTCGCCCGCGCCTACAACGACGACGGCGCCGATTCTTCGCT
GCTGCCGGACTTCCAAATGGCAGAAACCGTAGACAACTGGTGGAGTTTGGAGGACATCTGGTCACAGCAGCCGTACTGA

Alignment

ORF - retro_opun_37 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.85 %
• Parental protein coverage: 51.26 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TAAAAAAASEDEGDLRRGPWTVEEDMLLVDYIANHGEGRWNSLARCAGLRRTGKSCRLRWLNYLRPDVRR
          .AAAAA.A...E.DLRRGPWTVEED..L..Y.A..GEGRWN.LAR.AGLRRTGKSCRLRWLNYLRPDVRR
Retrocopy SAAAAAVAVAEEEDLRRGPWTVEEDAVLAGYVAANGEGRWNELARAAGLRRTGKSCRLRWLNYLRPDVRR

Parental  GNITADEQLLILDLHSRWGNRWSKIAQYLPGRTDNEIKNYWRTRVQKHAKQLRCDVNSKEFRDVVRHVWM
          G.....EQLLIL.LH.RWGNRWSKIAQ..PGRTDNEIKNYWRTRVQKHAKQL.CDVNS..F.D..RH.WM
Retrocopy GDFNPQEQLLILELHFRWGNRWSKIAQHMPGRTDNEIKNYWRTRVQKHAKQLGCDVNSRQFKDIMRHLWM

Parental  PRLVERIQADAAAATAGDVAAPP
          PRLVERIQA.A....A....A.P
Retrocopy PRLVERIQAAASSERAAPPCAVP

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Oryza punctata was not studied using ChIP-Seq data.

EST

Oryza punctata was not studied using EST data.

TSS

Oryza punctata was not studied using FANTOM5 data.

Lab

retro_opun_37 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza punctata 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.

---

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,