RetrogeneDB ID: retro_opun_41

Retrocopy location

• Organism: Red rice (Oryza punctata)
• Coordinates: 4:32223726..32225121(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OPUNC04G26580
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OPUNC04G26560
• Aliases: None
• Description: None

Sequence

>retro_opun_41
ATGGCAGGCGGCGGCGGCGGCAAGTCCGCCGCGGCGGCGCTGGCCATGGCCTGCTTCCTCCTCTTCCTCGCCGCCTTCGC
TCCCCCCGCAGCGGCGGCGCCGCCGGACATCATGTCGATCATCAGGTACAACGCGGAGCACGGGGTGCGGGGGCTGGAGG
TGGTGGAGCGGACGGAGGCCGAGGCGCGCGCCGTGTACGACCTGTGGGTGGCGCGGCACCGGCACGGCGGCGGCTCGCAC
AACGGGTTCGTCGGCGAGTACGAGCGCCGGTTCCGCGTGTTCTGGGACAACCTCAAGTTCGTCGACGCCCACAACGCCCA
CGCCGACGGGCACGGCGGGTTCCGCCTCGGGATGAACCGCTTCGCCGACCTCACCAACGACGAGTTCCGCGCCGCCTACC
TCGGCACCACGCCCGCCGGCAGGGGACGCCACGTCGGGGAGATGTACCGCCACGACGGCGTCGAGGCGCTGCCGGACTCC
GTGGACTGGAGGGACAAGGGCGCCGTCGTGTCCCCCGTAAAGAACCAGGGCCAGTGCGGTAGCTGCTGGGCGTTCTCGGC
GGTCGCCGCGGTGGAGGGCATCAACAAGATCGTCACCGGCGAGCTGGTGTCGCTGTCGGAGCAGGAGCTCGTGGAGTGCG
CAAGGAACGGGGGGAACAGCGGGTGCAACGGCGGGATCATGGACGACGCGTTCGCCTTCATCACCAGGAACGGCGGCCTC
GACACGGAGGAGGACTACCCGTACACCGCCATGGACGGCAAGTGCGACCTCGCCAAGAAGAGCCGCAAGGTGGTCTCCAT
CGACGGCTTCGAGGACGTGCCTGAGAACGACGAGCTGTCACTGCAGAAGGCCGTGGCGCACCAGCCCGTCAGCGTCGCCA
TCGACGCCGGCGGCCGCGAGTTCCAGCTCTACGACTCCGGCGTGTTCACCGGCCGGTGCGGCACGTCGCTGGACCACGGC
GTGGTGGCGGTGGGGTACGGCACGGACGCCGCCACCGGCACCGACTACTGGACGGTGCGCAACTCATGGGGACCCGACTG
GGGCGAGAACGGCTACATCCGCATGGAACGCAACGTCACCGCGCGCACCGGCAAGTGCGGCATCGCAATGATGGCGTCCT
ACCCGATCAAGAAGGGACCCAACCCGAAGCCATCACCGTCGCCGAAGCCATCGCCGCCGTCTCCAGCGCCATCGCCGCCG
CAGCAATGCGACCGCTACAGCAAGTGCCCGGCGGGAACCACATGCTGCTGCAACTATGGGATCAGGAACCACTGCATCGT
GTGGGGATGCTGCCCCGTCGAGGGCGCCACCTGCTGCAAGGATCACTCGACCTGCTGCCCCAAGGACTATCCGGTCTGCA
ACGCCAAGGCTCGGACTTGCTCCAAGGTATTTTAA

Alignment

ORF - retro_opun_41 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.85 %
• Parental protein coverage: 95.01 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AARAAAAFLLLLLV---GAASAAPD-MSIISYNAEHGARGL---ERTEAEARAAYDLWLAEN---GRSYN
          AA.A.A.FLL.L......AA.A.PD.MSII.YNAEHG.RGL...ERTEAEARA.YDLW.A.....G.S.N
Retrocopy AALAMACFLLFLAAFAPPAAAAPPDIMSIIRYNAEHGVRGLEVVERTEAEARAVYDLWVARHRHGGGSHN

Parental  A-LGERERRFRVFWDNLKFVDAHNARADEHGGFRLGMNRFADLTNDEFRSTFLGAKVVERSRAAGERYRH
          ...GE.ERRFRVFWDNLKFVDAHNA.AD.HGGFRLGMNRFADLTNDEFR...LG.....R.R..GE.YRH
Retrocopy GFVGEYERRFRVFWDNLKFVDAHNAHADGHGGFRLGMNRFADLTNDEFRAAYLGTTPAGRGRHVGEMYRH

Parental  DGVEELPESVDWREKGAV-APVKNQGQCGSCWAFSAVSTVESINQLVTGEMITLSEQELVECSTNGQNSG
          DGVE.LP.SVDWR.KGAV..PVKNQGQCGSCWAFSAV..VE.IN..VTGE...LSEQELVEC..NG.NSG
Retrocopy DGVEALPDSVDWRDKGAVVSPVKNQGQCGSCWAFSAVAAVEGINKIVTGELVSLSEQELVECARNGGNSG

Parental  CNGGLMDDAFDFIIKNGGIDTEDDYPYKAVDGKCDINRENAKVVSIDGFEDVPQNDEKSLQKAVAHQPVS
          CNGG.MDDAF.FI..NGG.DTE.DYPY.A.DGKCD......KVVSIDGFEDVP.NDE.SLQKAVAHQPVS
Retrocopy CNGGIMDDAFAFITRNGGLDTEEDYPYTAMDGKCDLAKKSRKVVSIDGFEDVPENDELSLQKAVAHQPVS

Parental  VAIEAGGREFQLYHSGVFSGRCGTSLDHGVVAVGYGTD--NGKDYWIVRNSWGPKWGESGYVRMERNINA
          VAI.AGGREFQLY.SGVF.GRCGTSLDHGVVAVGYGTD...G.DYW.VRNSWGP.WGE.GY.RMERN..A
Retrocopy VAIDAGGREFQLYDSGVFTGRCGTSLDHGVVAVGYGTDAATGTDYWTVRNSWGPDWGENGYIRMERNVTA

Parental  TTGKCGIAMMASYPTKSGANPPKPSPAP-PTPPTPPPPAAPDHVCDDNFSCPAGSTCCCAFGFRNLCLVW
          .TGKCGIAMMASYP.K.G.N.PKPSP.P.P.PP.P.P...P...CD....CPAG.TCCC..G.RN.C.VW
Retrocopy RTGKCGIAMMASYPIKKGPN-PKPSPSPKPSPPSPAP--SPPQQCDRYSKCPAGTTCCCNYGIRNHCIVW

Parental  GCCPVEGATCCKDHASCCPPDYPICNTRAGTCS
          GCCPVEGATCCKDH..CCP.DYP.CN..A.TCS
Retrocopy GCCPVEGATCCKDHSTCCPKDYPVCNAKARTCS

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_41 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza meridionalis	OMERI04G24530	1 retrocopy	retro_omer_32,
Oryza punctata	OPUNC04G26560	1 retrocopy	retro_opun_41 ,