RetrogeneDB ID: retro_oniv_34

Retrocopy location

• Organism: Indian wild rice (Oryza nivara)
• Coordinates: 8:88553..89270(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ONIVA08G00110
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ONIVA02G28050
• Aliases: None
• Description: None

Sequence

>retro_oniv_34
ATGGCGATGAAGGCGGTGATCAAGGGCGGCGATGGCGGAGGCGGGTGCATGGTGGTGGTGGCGCACGTGCTAGCGGTGGC
GGCGACGGCGATGGTGTTGGTGTGGTGCGTTCACTTCCGCGGCGGACTCGCCCTGCGCTCCCACAACAAGCAGCTCATCT
TCAACACCCACCCGGTGCTCATGGTGCTTGGCCTCGTCGTCCTCGCCGCCGAGGCCATCCTCTCCTACCGCTCCCTCTCC
ATCATCGTCAGCAGCAGGGACGCCAGAAAGAAGGTGCACCTGGGGCTGCACGCCGTGGGGCTCGCCCTCGGCGGCGTCGG
CATCTACGCGGTGTTCAAGTACCACGCCGAGGCCGACATCCCCAACCTCTACTCCCTCCACTCCTGGATCGGCATCGCCA
CCATCTCCCTCTACGCGCTCCACTGGCTCCTCGCCTTCCTCACCTTCTTCTTCCCCGGCGCCTCCCACGACACCAGGCGC
TCCGCCGTCCCGTGGCACGCGCTCCTCGGCCTCCTCGTCTTCGCGCTCGCCGTGGGCAACGCCCAGCTCGGCTTCCTCGA
GAAGCTCACCTTCCTGCAGGCCCCGCCGCTGCGCCTGTCCAGGTACGGGGCGGAGGCGCTACTCGTCAACTTCACGGCGC
TGGTGGTCCTCCTCCTCGGCGTCGCCGTCGTCCTCGCCACCGCCAACGTCGACTCCACTAAATACACCGCCATGTAA

Alignment

ORF - retro_oniv_34 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.67 %
• Parental protein coverage: 88.03 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VAHALAVAAATMVLVWCIHFRGGLAFEATNKNLIFNVHPVLMLIGYIILGSEAIMVYKVLP--TWKHDTT
          VAH.LAVAA..MVLVWC.HFRGGLA....NK.LIFN.HPVLM..G...L..EAI..Y..L.......D..
Retrocopy VAHVLAVAATAMVLVWCVHFRGGLALRSHNKQLIFNTHPVLMVLGLVVLAAEAILSYRSLSIIVSSRDAR

Parental  KLIHLILHAIALVFGAVGIYCAFKFHNESGIANLYSLHSWLGIGTICLYGIQWIFGFVAFFFPRASPSVR
          K..HL.LHA..L..G.VGIY..FK.H.E..I.NLYSLHSW.GI.TI.LY...W...F..FFFP.AS...R
Retrocopy KKVHLGLHAVGLALGGVGIYAVFKYHAEADIPNLYSLHSWIGIATISLYALHWLLAFLTFFFPGASHDTR

Parental  KGVLPWHILFGLFVYILALATVELGFLEKLTFLQSS--GLDKYGAEAFLVNFTALIVVLFGASVVVAAVS
          ....PWH.L.GL.V..LA.....LGFLEKLTFLQ.....L..YGAEA.LVNFTAL.V.L.G..VV.A...
Retrocopy RSAVPWHALLGLLVFALAVGNAQLGFLEKLTFLQAPPLRLSRYGAEALLVNFTALVVLLLGVAVVLATAN

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Oryza nivara was not studied using ChIP-Seq data.

EST

Oryza nivara was not studied using EST data.

TSS

Oryza nivara was not studied using FANTOM5 data.

Lab

retro_oniv_34 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza nivara 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,