RetrogeneDB ID: retro_oruf_27

Retrocopy location

• Organism: Brownbeard rice (Oryza rufipogon)
• Coordinates: 1:27532113..27532938(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ORUFI01G32240
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ORUFI01G24440
• Aliases: None
• Description: None

Sequence

>retro_oruf_27
ATGGCCGGGATCGTGGTGGTGTTCGACTTCGACAAGACGATCATCGACGTCGACAGCGACAACTGGGTCGTGGACGGGCT
CGGCGCGACGGAGGAGTTCGAGCGGCTGCTGCCCACCATGCCGTGGAACACCCTCATGGACACCATGATGGGCGAGCTCC
ACGCGCGCGGCAAGACCCTCGGCGACGTCGCGGCGGTGCTCAGGTCGGCGCCGCTCGACCCGCGCGTCGTCGCCGCCATC
AAGGCCTGCTACGGCCTCGGCTGCGACCTCCGGATCCTCAGCGACGCCAACCGCTTCTTCATCGACACCATCCTCGACCA
CCACGGCCTCACGGGTTACTTCTCCGAGATCAACACCAACCCGAGCGCCGTCGACGCCGCCACCGGCCGCCTCCGCATCG
CGCCGTACCACGACTTCCACGCCGGCCCGCACGGGTGCGGCCTCGGGATCTGCCCGCCCAACATGTGCAAGGGCCAGGTG
CTCGACCGCATCCGCGCCTCCGCCGGCGCCGCCGGCAAGAGGGTCATCTACCTCGGCGACGGCCGCGGCGACTACTGCCC
GTCGCTCCGCCTCGGCCGCGACGACTTCATGATGCCACGCAGGGGCTTCCCCGTGTGGGAGCTCATCTGCGAGGACCCGT
CGCTGCTCCAAGCGGAGGTGCACCCGTGGGCCGACGGCGCCGAGATGGAGGAGACGCTGCTGCGGCTGGTCGGCAGGGTG
CTCCTCGAGGAGAGGAACCTGCCGCCGCTCGACTGCAAGCTCGAGTCGTTGCCGGCCGTCGCCGTGCAGGACGGCATGCC
CATGACGCTCCGGATCAAGAACTGA

Alignment

ORF - retro_oruf_27 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.43 %
• Parental protein coverage: 92.61 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GVVVVFDFDRTIIEWDSDDWVITKLGASDAFRRLRPTMRWNPLMDRMMVELHAQGRSADDIRDCLKSAPL
          G.VVVFDFD.TII..DSD.WV...LGA...F.RL.PTM.WN.LMD.MM.ELHA.G....D....L.SAPL
Retrocopy GIVVVFDFDKTIIDVDSDNWVVDGLGATEEFERLLPTMPWNTLMDTMMGELHARGKTLGDVAAVLRSAPL

Parental  DAHVLSAITTASALGCDLRVASDANAFFIETVLEHHGVLGCFSEISTNPARVD-GNGRLRISPFHDPDDS
          D..V..AI.....LGCDLR..SDAN.FFI.T.L.HHG..G.FSEI.TNP..VD...GRLRI.P.HD....
Retrocopy DPRVVAAIKACYGLGCDLRILSDANRFFIDTILDHHGLTGYFSEINTNPSAVDAATGRLRIAPYHD-FHA

Parental  SPHGCSL--CPENMCKGKIIERIQATANGK-RHFIYIGDGRGDYCPSLKLGEGDYVMPKENYPLWNLISS
          .PHGC.L..CP.NMCKG....RI.A.A.......IY.GDGRGDYCPSL.LG..D..MP....P.W.LI..
Retrocopy GPHGCGLGICPPNMCKGQVLDRIRASAGAAGKRVIYLGDGRGDYCPSLRLGRDDFMMPRRGFPVWELICE

Parental  NKQLLKAEVHPWNNGEELEQTLLKLVNKLITPPAQPSQFEYKCDMSNPVSTEVGQAL
          ...LL.AEVHPW..G.E.E.TLL.LV...............K......V....G...
Retrocopy DPSLLQAEVHPWADGAEMEETLLRLVGRVLLEERNLPPLDCKLESLPAVAVQDGMPM

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_27 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 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA001283	1 retrocopy	retro_oind_8,
Brachypodium distachyon	BRADI2G42720	1 retrocopy	retro_bdis_19,
Zea mays	GRMZM2G035134	1 retrocopy	retro_zmay_14,
Hordeum vulgare	MLOC_52823	1 retrocopy	retro_hvul_27,
Oryza brachyantha	OB01G31280	1 retrocopy	retro_obra_4,
Oryza glumaepatula	OGLUM01G25430	1 retrocopy	retro_oglu_22,
Oryza meridionalis	OMERI01G19970	1 retrocopy	retro_omer_22,
Oryza nivara	ONIVA01G24910	1 retrocopy	retro_oniv_37,
Oryza punctata	OPUNC01G21870	1 retrocopy	retro_opun_7,
Oryza rufipogon	ORUFI01G24440	1 retrocopy	retro_oruf_27 ,