RetrogeneDB ID: retro_opun_18

Retrocopy location

• Organism: Red rice (Oryza punctata)
• Coordinates: 7:30954074..30955832(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OPUNC07G25670
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OPUNC03G13130
• Aliases: None
• Description: None

Sequence

>retro_opun_18
ATGGAGAGCACCGGCGGAGGATCTCCCAAGGAGGCGGTGGTGCCGTCCGCTGCCTCCGGCGACGCCACTCTGGGCGGGCA
CCTGGCTCGCCGCCTCGTGCAGGTGGGCGTCAGCGACGTGTTCGCCGTGCCCGGGGACTTCAACCTCACGCTTCTCGACC
ACCTCATCGCCGAGCCCGGGCTCCGCGTCGTCGGATGCTGCAACGAGCTCAACGCCGGCTACGCCGCCGACGGGTACGCG
CGGGCCCGTGGCGTGGGCGCCTGCGCCGTGACCTTCACCGTCGGCGGGCTGAGCGTGCTGAACGCCATCGGCGGCGCGTA
CAGCGAGAACCTGCCGCTGATCTGCATCGTGGGGGGCCCAAACTCCAACGACTACGGCACCAACCGCATCCTCCACCACA
CCATCGGCCTCCCGGACTTCTCCCAGGAGCTCCGCTGCTTCCAGCCCCTCACCTGCTACCAGGCCGTCGTCAACAACCTC
GACGATGCCCACGAGCAGATCGACCGCGCCATCTCCACCGCCATCCGGGAGAGCAAGCCCGTCTACATCAGCGTCAGCTG
CAACCTCCCCGGTGTCCCGCACCCCACCTTCTCCCGCGACCCCGTCCCCTACTTCCTCTCCCCGAGGCTCTCCAACCAGG
CCAGCCTCGACGCCGCGCTCCACGCCACCCTCGCCTTCCTCGACAAGGCCGTCAAGCCCGTCCTCGTCGCCGGCCCCAAG
CTCCGCGTCGCCAAGGCGGGAGGGGCCTTCGCCGACCTCGCCGACGCCAGCGGCTACGCGGTGGCCGCCATGCCGTCCGC
CAAGGGCCTCGTGCCGGAGACGCTGCCGCGGTTCATCGGCACCTACTGGGGCGCCGTCAGCACGGCCTTCTGCGCCGAGA
TCGTCGAGTCCGCCGACGCCTACCTCTTCGCGGGGCCCATCTTCAACGACTACAGCTCCGTCGGGTACTCGTGCCTCCTG
AAGAAGGAGAAGGCGGTGGTGGTGCAGCCCGACCGCGTGACCATCGGCAATGGCCCGGCGTTCGGGTGCGTCATGATGAA
GGACTTTCTGTCGGAGCTGGCCAAGCGCGTCCGGAAGAACACGACGGCGTTCGACAACTACAGGAGGATCTTCGTGCCGG
ATGGGCAGCTGCCGGAGTGCGAGGCCGGCGAGCCGCTGCGGGTGAACGTGCTGTTCAAGCACATACAGAGGATGATCGGC
GGGGAGGAGATCGGGGCGGTGATGGCGGAGACGGGAGACTCGTGGTTCAACTGCCAGAAGCTGCGGCTGCCCGAGGGTTG
CGGGTACGAGTTCCAGATGCAGTACGGCTCCATCGGGTGGTCGGTGGGGGCGCTGCTGGGCTACGCGCAGGCTGTCCAGA
AGCGGGTGGTGGCTTGCATCGGCGACGGCAGCTTCCAGGTGACGGCGCAGGACGTGTCCACGATGCTGCGTTGCGGCCAG
CGGAGCATCATCTTCCTCATCAACAACGGCGGCTACACCATCGAGGTGGAGATCCACGACGGGCCGTACAACGTGATCAA
GAACTGGGACTACGTCGGCCTCGTCAACGCCATCCACAACGGCGACGGCCGGTGCTGGGCGACCAGGGTGCGGTGCGAGG
AGGAGCTGGAGGCGGCGATCGCGACGGCGACGGGGGACAAGGCGGACAGCCTGTGCTTCATCGAGGTGGTGGCGCACAAG
GACGACACCAGCAAGGAGCTTCTGGAATGGGGCTCAAGGGTCTCCGCCGCCAACTCCAGGCCGCCCAACCCGCAGTAG

Alignment

ORF - retro_opun_18 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.42 %
• Parental protein coverage: 94.74 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SARPAAVPVSA-GEASLGRHLARRLVQVGVSDVFAVPGDFNLTLLDHLIAEPGLRLVGCCNELNAGYAAD
          S...A.VP..A.G.A.LG.HLARRLVQVGVSDVFAVPGDFNLTLLDHLIAEPGLR.VGCCNELNAGYAAD
Retrocopy SPKEAVVPSAASGDATLGGHLARRLVQVGVSDVFAVPGDFNLTLLDHLIAEPGLRVVGCCNELNAGYAAD

Parental  GYARARGVGACAVTFTVGGLSVLNAIAGAYSENLPVICIAGGPNSNDYGTNRILHHTIGLPDFSQELRCF
          GYARARGVGACAVTFTVGGLSVLNAI.GAYSENLP.ICI.GGPNSNDYGTNRILHHTIGLPDFSQELRCF
Retrocopy GYARARGVGACAVTFTVGGLSVLNAIGGAYSENLPLICIVGGPNSNDYGTNRILHHTIGLPDFSQELRCF

Parental  QTVTCHQAVVTNLEDAHEQIDTAIATALRESKPVYLSISCNLPGLPHPTFSRDPVPFFLSPRLSNKMGLE
          Q..TC.QAVV.NL.DAHEQID.AI.TA.RESKPVY.S.SCNLPG.PHPTFSRDPVP.FLSPRLSN...L.
Retrocopy QPLTCYQAVVNNLDDAHEQIDRAISTAIRESKPVYISVSCNLPGVPHPTFSRDPVPYFLSPRLSNQASLD

Parental  AAVEATVEFLNKAVKPVLVGGPKLRVAKAGKAFVDLVDASGYAYAVMPSAKGLVPETHPHFIGTYWGAVS
          AA..AT..FL.KAVKPVLV.GPKLRVAKAG.AF.DL.DASGYA.A.MPSAKGLVPET.P.FIGTYWGAVS
Retrocopy AALHATLAFLDKAVKPVLVAGPKLRVAKAGGAFADLADASGYAVAAMPSAKGLVPETLPRFIGTYWGAVS

Parental  TAFCAEIVESADAYLFAGPIFNDYSSVGYSFLLKKDKAIIVQPERVIVGNGPAFGCVMMKEFLSELAKRV
          TAFCAEIVESADAYLFAGPIFNDYSSVGYS.LLKK.KA..VQP.RV..GNGPAFGCVMMK.FLSELAKRV
Retrocopy TAFCAEIVESADAYLFAGPIFNDYSSVGYSCLLKKEKAVVVQPDRVTIGNGPAFGCVMMKDFLSELAKRV

Parental  NKNTTAYENYKRIFVPEGQPLESEPNEPLRVNVLFKHVQKMLNRD--SAVIAETGDSWFNCQKLKLPEGC
          .KNTTA..NY.RIFVP.GQ..E.E..EPLRVNVLFKH.Q.M.......AV.AETGDSWFNCQKL.LPEGC
Retrocopy RKNTTAFDNYRRIFVPDGQLPECEAGEPLRVNVLFKHIQRMIGGEEIGAVMAETGDSWFNCQKLRLPEGC

Parental  GYEFQMQYGSIGWSVGALLGYAQGAKDKRVIACIGDGSFQVTAQDVSTMLRCAQNSIIFLINNGGYTIEV
          GYEFQMQYGSIGWSVGALLGYAQ.A..KRV.ACIGDGSFQVTAQDVSTMLRC.Q.SIIFLINNGGYTIEV
Retrocopy GYEFQMQYGSIGWSVGALLGYAQ-AVQKRVVACIGDGSFQVTAQDVSTMLRCGQRSIIFLINNGGYTIEV

Parental  EIHDGPYNVIKNWNYTGLVDAIHNGEGKCWTSKVKCEEELTDAISTALGEKKDCMCFIEVIAHKDDTSKE
          EIHDGPYNVIKNW.Y.GLV.AIHNG.G.CW...V.CEEEL..AI.TA.G.K.D..CFIEV.AHKDDTSKE
Retrocopy EIHDGPYNVIKNWDYVGLVNAIHNGDGRCWATRVRCEEELEAAIATATGDKADSLCFIEVVAHKDDTSKE

Parental  LLEWGSRVSAANSRPPNPQ
          LLEWGSRVSAANSRPPNPQ
Retrocopy LLEWGSRVSAANSRPPNPQ

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_18 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Zea mays	GRMZM2G087186	1 retrocopy	retro_zmay_12,
Oryza barthii	OBART03G13620	1 retrocopy	retro_obar_6,
Oryza glumaepatula	OGLUM03G13720	1 retrocopy	retro_oglu_28,
Oryza meridionalis	OMERI02G33690	1 retrocopy	retro_omer_19,
Oryza punctata	OPUNC03G13130	1 retrocopy	retro_opun_18 ,
Oryza rufipogon	ORUFI03G14280	1 retrocopy	retro_oruf_25,