RetrogeneDB ID: retro_opun_38

Retrocopy location

• Organism: Red rice (Oryza punctata)
• Coordinates: 7:16115562..16117038(+)
• Located in intron of: OPUNC07G11360

Retrocopy information

• Ensembl ID: OPUNC07G11370
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OPUNC07G06140
• Aliases: None
• Description: None

Sequence

>retro_opun_38
ATGGCGGCGGCGGCGGTGGCGGCGGATCGGAAGGTGTTGGTGACGAGGCTCTGCGAGGGCTGCGCTTGCGCCGCGCCTGC
TGCACCGCGGGTGCCGAAGATGGCGGCGGCGCAGAGGGTGGTGGCGGAGCTGAGAGAGGCGTGCGCGACGCCGGTGGCGA
GGCTGGCGGAGGTGGCCGCGGCGATGGCCGGGGAGATGGAGGCCGGGCTGGCGGTGGAGGGCGGAAGCAGCAAGATGAAG
ATGATCGTGTCGTACGTCGACAGCCTCCCCAACGGCGGTGAGGAGGGGTCGTTCTACGCCCTCGACCTCGGCGGCACAAA
CTTCCGCGTCCTCCGCGTGCGCCTCGCCGGCGGCAGCGTCGCCGAGCGCGTGGCGAGGGAGGTCCCGATCCCTCCTGGCC
TCATGTCCGGCGACGGCGCCACCTCGGAACGCCTCTTCGGTTTCGTCGCCTCCGCGCTAGCCGAGTTCGTCGCCGAGGAG
GAAGAAGGCCACGACGGCGGCAAGAGGGAGCTTGGGTTCACCTTCTCCTTCCCCGTGCACCAAACCTCCATCGCGTCGGG
GACGCTCATCCGGTGGACGAAGGCGTTCGCCGTCGATGACGCCGTTGGCGAGGACGTGGTGGCGGCGCTGCAGGCTGCCA
TGTCGAAGCAGGGGCTCGACATCCGCGTGTCGGCGCTCATCAACGACACCGTCGGGACGCTCGCCGCGGGCAGCTACTAC
GACGAGGACGTCGTGGCCGCCGTCATCCTCGGCACAGGCACGAACGCCGCCTACGTCGAGGACGCCACCGCCATCGCGAA
GCTACAGCCCACGCAGCTACCAGCATCAAACATCATGGTGATCAACACCGAGTGGGGCAGCTTCGCCTCGCCGTGCCTCC
CATTAACGGAGTTCGACGAAGCACTCGATGAGGAGAGCCTCAACCCCGGCGAGCAAACCTACGAGAAGCTCATCTCCGGG
ATGTACCTCGGCGAGATCGTGAGGAGGGTCCTCCTCAAGATCTCCTCCCGGTGCTCCTCCTTCTTCAGAGCCAGCGCCGG
CGCCGGCGAGCTCATGACACCGTTCGTCCTCAATACACCCGACGTCTCGGCGATGCACCACGACGAGACGCCCGACCTGA
GCATCGTCGGCGAGAAGCTGGCACACACGCTGAGCATCGACGGCACGTCGCTGGAGACGAGGAGGATGGTCGTCGAGGTG
TGCGACATCGTCGCCACGAGGGCCGCCCGGCTGGCCGCGGCCGGGATCGTCGGGATCCTGAAGAAGATCGGGAGAGGCGG
CGACGGGCAGAGGTCGGTGGTCGCCGTCGACGGCGGGCTGTTCGAGCACTACGGCAAGTTCCGGCGGTGCATGGAGAGCA
CCGTGAGCGAGCTGCTCGGAGAGAAGGCGGCGCAGAGGGTGGTCGTCAAGCTCGCCAGCGACGGCTCCGGGCTCGGCGCC
GCCCTGGTTGCAGCTGCTCACTCGCAGAGAGCATAA

Alignment

ORF - retro_opun_38 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.18 %
• Parental protein coverage: 94.59 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GCAAAVRCSAVAPTSAVAP-ILADLRQRCAAPLPVLRRVADAMAAGMRAGLAADG-AGELKMIPSHVYSL
          GCA.A.......P..A.A....A.LR..CA.P...L..VA.AMA..M.AGLA..G.....KMI.S.V.SL
Retrocopy GCACAAPAAPRVPKMAAAQRVVAELREACATPVARLAEVAAAMAGEMEAGLAVEGGSSKMKMIVSYVDSL

Parental  PTGNETGLFYALDLGGTNFRVLRVQLGGKDKRIIDTEFEQVSIPNEIMHG---TTEDLFDFIASGLSRFV
          P.G.E.G.FYALDLGGTNFRVLRV.L.G............V.IP...M.G...T.E.LF.F.AS.L..FV
Retrocopy PNGGEEGSFYALDLGGTNFRVLRVRLAGGS--VAERVAREVPIPPGLMSGDGATSERLFGFVASALAEFV

Parental  ATEGDKCHLPQGRKREIGFTFSFPVNQTSIDSGILIKWTKGFAVSGTAGKDVVACLNAAMERQGLDMRVS
          A.E....H...G.KRE.GFTFSFPV.QTSI.SG.LI.WTK.FAV....G.DVVA.L.AAM..QGLD.RVS
Retrocopy AEE-EEGH--DGGKRELGFTFSFPVHQTSIASGTLIRWTKAFAVDDAVGEDVVAALQAAMSKQGLDIRVS

Parental  ALVNDTVGTLAGAHYWDDDVMVAVILGTGTNACYIQRTEAIPKLQHLKLGTGNT-IINTEWGAF-SDGLP
          AL.NDTVGTLA...Y.D.DV..AVILGTGTNA.Y.....AI.KLQ...L...N...INTEWG.F.S..LP
Retrocopy ALINDTVGTLAAGSYYDEDVVAAVILGTGTNAAYVEDATAIAKLQPTQLPASNIMVINTEWGSFASPCLP

Parental  LTEFDREMDDESINPGEQIFEKTISGMYLGEIV-RRVLVKMAEVSDLFGHSFPK-KLAEPFVLRTPHLCA
          LTEFD...D.ES.NPGEQ..EK.ISGMYLGEIV.R..L......S..F..S.....L..PFVL.TP...A
Retrocopy LTEFDEALDEESLNPGEQTYEKLISGMYLGEIVRRVLLKISSRCSSFFRASAGAGELMTPFVLNTPDVSA

Parental  MQQDNSDNLGEVESILSDIIGVSQASLPARRVAVQVSDCIIRRGGRLAGAGIVGILEKMENDSEGQIFGR
          M..D....L..V...L.........SL..RR..V.V.D....R..RLA.AGIVGIL.K......GQ....
Retrocopy MHHDETPDLSIVGEKLAHTLSIDGTSLETRRMVVEVCDIVATRAARLAAAGIVGILKKIGRGGDGQ----

Parental  RTVVAMDGGLYEKYPQYRRYMKEAVAELLGPGQSNHITIEHTKDGSGIGAALLAAANSKYA
          R.VVA.DGGL.E.Y...RR.M...V.ELLG.............DGSG.GAAL.AAA.S..A
Retrocopy RSVVAVDGGLFEHYGKFRRCMESTVSELLGEKAAQRVVVKLASDGSGLGAALVAAAHSQRA

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_38 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryza punctata	OPUNC07G06140	1 retrocopy	retro_opun_38 ,