RetrogeneDB ID: retro_oniv_4

Retrocopy location

• Organism: Indian wild rice (Oryza nivara)
• Coordinates: 4:12846867..12848181(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ONIVA04G09540
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ONIVA03G14420
• Aliases: None
• Description: None

Sequence

>retro_oniv_4
ATGGCCGCGGCGAGTTTGATCAAGGCGCCCGTGGGGCAGAATCCTGCGAGGATGGGCTCGGGGAGGAGCAGCGGAGGAGG
AGGGGTGGTCAGGTGCTCGCTGCAGGGCGCCGTGGTGGGCGGCCGGGCGGAGTGGCAGAGCAGCTGCGCCGTGCTGTCCA
GCAAGGTGGCCGCGCTCGGGGCGGCGTCCCCGCACGCCGCGGCGCCAAGCTTCGTTAATGGGCATGTCGCGCCGCTGGTC
CCGGAGCAGCCGGCGGCGGCGGCGGAGGACGGCGGGGCGGTGCTGGATTTGGTGCCCGTGAGCAGCGTTAATGGCGGGGG
CGTCGCCAAGAACCTGCCGCAGCCGCTGCGGATCTCGGATCTGTCGCCGGCGCCGATGCACGGGTCGCAGCTGCGCGTGG
CGTACCAGGGCGTCCCCGGTGCGTACAGCGAGAAGGCGGCCGGGAAGGCGTACCCGGGCTGCGATGCCATCCCCTGCGAC
CAGTTCGAGGTGGCGTTCTCGGCCGTGGAGCTGTGGATCGCCGACCGCGCCGTGCTCCCCGTGGAGAACTCGCTGGGCGG
CAGCATCCACCGCAACTACGACCTCCTGCTCAGGCACCGGCTCCACATCGTCGGCGAGGTGCAGCTCCCCGTGCACCACT
GCCTCATGGCGCTCCCGGGGGTCCGCAAGGAGTGCCTCACCCGCGTGATGAGCCACCCGCAGGCGCTGGCGCAGTGCGAG
CACACGCTCACCGCCATGGGGCTCAACGTCGTCCGCGAGGCCTTCGACGACACCGCGGGCGCCGCCGAGTACGTCGCCGC
CAACGGCCTCCGCGACACGGCCGCCATCGCCTCCTCCCGCGCCGCCGAGCTTTACGGCATGGAGGTGCTCGCCGACGGCA
TCCAGGACGACTGCGGCAACGTCACCCGCTTCGTCATGCTCGCCCGCGAGCCCATCGTGCCCCGCACCGACCGCCCCTTC
AAGACCAGCATCGTGTTCGCCCACGACAAGGAGGGCACCTCCGTCCTCTTCAAGGTCCTCTCCGCCTTCGCCTTCCGCGA
CATCACCCTCACCAAGATCGAGAGCCGCCCGCACCGCCACCGCCCCATCCGCCTCGTCGACGACGCCAACGTCGGCACCG
CCAAGCACTTCGAGTACATGTTCTACGTCGACTTCCAGGCCTCCCTCGCCGAGCCCCGCGCGCAGAACGCGCTCGCCGAG
GTGCAGGAGTACACCTCCTTCCTCCGGGTGCTCGGCAGCTACCCCATGGACATGACCCCCATGACCGCCGGCTCCTCCTC
CACCGTCACCTCCGACGATTCCTCCTCCACTTGA

Alignment

ORF - retro_oniv_4 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.36 %
• Parental protein coverage: 71.39 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LPRPLTSADLMG--VSGEGLKVAYQGCPGAYSEAAAKKAYPNCQTVPCEHFDTAFKAVENWLADRAVLPL
          LP.PL...DL......G..L.VAYQG.PGAYSE.AA.KAYP.C...PC..F..AF.AVE.W.ADRAVLP.
Retrocopy LPQPLRISDLSPAPMHGSQLRVAYQGVPGAYSEKAAGKAYPGCDAIPCDQFEVAFSAVELWIADRAVLPV

Parental  ENSLGGSIHRNFDLLLRHRLHIVGEVRLAVRHCLLANPGVKIENLKSAMSHPQALAQCEHTLTEFGIE-H
          ENSLGGSIHRN.DLLLRHRLHIVGEV.L.V.HCL.A.PGV..E.L...MSHPQALAQCEHTLT..G....
Retrocopy ENSLGGSIHRNYDLLLRHRLHIVGEVQLPVHHCLMALPGVRKECLTRVMSHPQALAQCEHTLTAMGLNVV

Parental  REAVDDTAGAAKTVAEQNLPDTGAIASSLAAELYGLNVLAENIQDDKDNVTRFMMLAREPIIPRTDKPFK
          REA.DDTAGAA..VA...L.DT.AIASS.AAELYG..VLA..IQDD..NVTRF.MLAREPI.PRTD.PFK
Retrocopy REAFDDTAGAAEYVAANGLRDTAAIASSRAAELYGMEVLADGIQDDCGNVTRFVMLAREPIVPRTDRPFK

Parental  TSIVFSLE-EGPGQLFKALGVFALREINLTKIESRPHKKRPLRITDDSFSTPSKQFDYLFYMDLEASMAD
          TSIVF....EG...LFK.L..FA.R.I.LTKIESRPH..RP.R..DD......K.F.Y.FY.D..AS.A.
Retrocopy TSIVFAHDKEGTSVLFKVLSAFAFRDITLTKIESRPHRHRPIRLVDDANVGTAKHFEYMFYVDFQASLAE

Parental  PKTQNALGNLKEFATFLRVLGSYPTD
          P..QNAL....E...FLRVLGSYP.D
Retrocopy PRAQNALAEVQEYTSFLRVLGSYPMD

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_4 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Amborella trichopoda	AMTR_s00080p00093010	1 retrocopy	retro_atri_11,
Oryza nivara	ONIVA03G14420	1 retrocopy	retro_oniv_4 ,
Oryza glaberrima	ORGLA03G0127300	1 retrocopy	retro_ogla_17,
Oryza rufipogon	ORUFI03G13820	1 retrocopy	retro_oruf_22,