RetrogeneDB ID: retro_opun_42

Retrocopy location

• Organism: Red rice (Oryza punctata)
• Coordinates: 8:141637..142363(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OPUNC08G00200
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OPUNC02G23460
• Aliases: None
• Description: None

Sequence

>retro_opun_42
ATGGCGCAGCTCATCAAGGGCGGTGGTGGTCATGGCGGCGGCGGCGGCGGCGGGTTCATGGTGTTGGTGGCGCACGTGCT
AGCGGTGGCGGCGACGGCGATGGTGGTGGTGTGGTGCGTCCACTTCCGCGGCGGACTCGCCCTGCGCTCCCACAACAAGC
AGCTCATCTTTAACACTCACCCGGTGCTTATGCTGATCGGCCTCGTCGTCGTCGCCGCCGAGGCCATCCTCTCCTACCGC
TCCCTCTCCATGATCAGCAGCAGCAGGGACGCCAGGAAGAAGACGCACCTGGCGCTGCACGCCGTCGCCCTCGCCCTCGG
CGGCCTCGGCATCTACGCGGTGTTCAAGTACCACGCCGAGGCCGACATCCCCAACCTCTACTCGCTCCACTCCTGGATCG
GCATCGTCACCATCTCCCTCTACGCGCTTCACTGGATCGTCGCCTTCCTCACCTTCTTCTTCCCCGGCGCCTCCCACAAC
ACCAGGCGCTCCGCCGTGCCGTGGCACGCGCTCCTCGGCCTCCTCGTCTTCGCGCTCGCCGTCGGCAACGCGCAGCTCGG
CTTCCTGGAGAAGCTCACCTTCCTGCAGGCCCCGCCGCTCCGCCTCTCCAGGTACGGCCCGGAGGCGCTGCTCGTCAACT
TCACGGCGCTCGTGGTCCTCCTCCTCGGCGTCGCCGTCGTTCTCGCCACCGCCAACGTCGACTCCACTAAATACACCGCC
ATGTAA

Alignment

ORF - retro_opun_42 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.1 %
• Parental protein coverage: 88.03 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VAHALAVAAAAMVLVWCIHFRGGLAFEATNKNLIFNVHPVLMLIGYIILGSEAIMVYKVLP--TWKHDTT
          VAH.LAVAA.AMV.VWC.HFRGGLA....NK.LIFN.HPVLMLIG......EAI..Y..L.......D..
Retrocopy VAHVLAVAATAMVVVWCVHFRGGLALRSHNKQLIFNTHPVLMLIGLVVVAAEAILSYRSLSMISSSRDAR

Parental  KLIHLILHAIALVLGAIGIYCAFKFHNESGIANLYSLHSWLGIGTICFYSIQWIFGFVAFFFPRASPSVR
          K..HL.LHA.AL.LG..GIY..FK.H.E..I.NLYSLHSW.GI.TI..Y...WI..F..FFFP.AS...R
Retrocopy KKTHLALHAVALALGGLGIYAVFKYHAEADIPNLYSLHSWIGIVTISLYALHWIVAFLTFFFPGASHNTR

Parental  KGVLPWHILFGLFVYILALATAELGFLEKLTFLQSS--GLDKYGAEAFLVNFTALVVVLFGASVVVAAVS
          ....PWH.L.GL.V..LA...A.LGFLEKLTFLQ.....L..YG.EA.LVNFTALVV.L.G..VV.A...
Retrocopy RSAVPWHALLGLLVFALAVGNAQLGFLEKLTFLQAPPLRLSRYGPEALLVNFTALVVLLLGVAVVLATAN

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_42 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.

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA005956	1 retrocopy	retro_oind_56,
Oryza brachyantha	OB02G32980	1 retrocopy	retro_obra_5,
Oryza barthii	OBART02G25610	1 retrocopy	retro_obar_22,
Oryza glumaepatula	OGLUM02G26140	1 retrocopy	retro_oglu_26,
Oryza nivara	ONIVA02G28050	1 retrocopy	retro_oniv_34,
Oryza punctata	OPUNC02G23460	1 retrocopy	retro_opun_42 ,
Oryza rufipogon	ORUFI02G27020	1 retrocopy	retro_oruf_43,
Physcomitrella patens	PP1S194_18V6	1 retrocopy	retro_ppat_14,