RetrogeneDB ID: retro_oglu_28

Retrocopy location

• Organism: Oryza glumaepatula
• Coordinates: 7:28117972..28119736(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OGLUM07G27300
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OGLUM03G13720
• Aliases: None
• Description: None

Sequence

>retro_oglu_28
ATGGAGAGCAACGGCGGAGGAGGAGGATCTCCCAAGGAGGCAGCGGTGGTGGTGCCGTCCTCCGGCGACGCCACACTGGG
CGGGCACCTGGCGCGGCGCCTCGTGCAGGTGGGCGTGAGCGACGTGTTCGCCGTGCCGGGGGACTTCAACCTGACGCTTC
TGGACCACCTGATCGCCGAGCCCGGGCTCCGCGTGGTGGGCTGCTGCAACGAGCTGAACGCCGGATACGCGGCCGACGGG
TACGCGCGGGCCCGTGGCGTGGGCGCCTGCGCCGTGACCTTCACCGTGGGCGGGCTGAGCGTGCTGAACGCCATCGGCGG
CGCGTACAGCGAGAACCTGCCGCTGATCTGCATCGTGGGGGGCCCAAACTCCAACGACTACGGCACCAACCGCATCCTCC
ACCACACCATCGGCCTCCCGGACTTCTCCCAGGAGCTCCGCTGCTTCCAGCCCCTCACCTGCTACCAGGCCGTCGTCAAC
AACCTCGACGACGCCCACGACCAGATCGACCGCGCCATCTCCACCGCCATCAGGGAGAGCAAGCCCGTCTACATCAGCGT
CAGCTGCAACCTCCCCGCCGTCCCCCACCCCACCTTCTCCCGCGACCCGGTGCCCTACTTCCTCTCCCCGAGGCTCTCCA
ACCAGGCCAGCCTCCACGCCGCGCTCGACGCCACCCTCGCCTTCCTCGACAAGGCCGTCAAGCCCGTCCTCGTCGCGGGG
CCCAAGCTCCGCGTCGCCAAGGCCGGAGGGGCCTTCGTGGACCTCGCCGACGCCAGCGGCTACGCGGTGGCCGCCATGCC
GTCCGCCAAGGGGCTGGTGCCGGAGACGCTGCCGCGCTTCATCGGGACCTACTGGGGCGCGGTCAGCACGGCCTTCTGCG
CGGAGATCGTGGAGTCCGCGGACGCCTACCTGTTCGCGGGGCCCATCTTCAACGACTACAGCTCCGTGGGGTACTCGTGC
CTGCTGAAGAAGGAGAAGGCGGTGGTGGTGCAGCCCGACCGCGTGACCATCGGCAATGGCCCCGCGTTCGGGTGCGTGAT
GATGAGGGACTTCCTGTCGGAGCTGGCCAAGCGCGTCCGGAAGAACACGACGGCGTTCGACAACTACAAGAGGATCTTCG
TGCCGGAGGGGCAGCTGCCGGAGTGCGAGGCCGGGGAGGCGCTGCGGGTGAACGTGCTGTTCAAGCACATACAGAGGATG
ATCGGTGGCGCGGAGATCGGGGCGGTGATGGCGGAGACGGGGGACTCGTGGTTCAACTGCCAGAAGCTGCGGCTGCCCGA
GGGTTGCGGGTACGAGTTCCAGATGCAGTACGGCTCCATCGGGTGGTCGGTGGGGGCGCTGCTGGGCTACGCGCAGGCTG
TCCAAAAACGGGTGGTGGCTTGCATCGGCGACGGCAGCTTCCAGGTGACGGCGCAGGACGTGTCGACGATGCTGCGTTGC
GGGCAGCGGAGCATCATCTTCCTCATCAACAACGGCGGGTACACCATCGAGGTGGAGATCCACGACGGGCCGTACAACGT
GATCAAGAACTGGGACTACGTGGGCCTCGTCAACGCCATCCACAACGGCGAGGGGCGGTGCTGGGCCACCCGGGTGCGGT
GCGAGGAGGAGCTGGAGGCGGCCATCGCGACGGCCACGGGGGACAAGGCGGACAGCCTCTGCTTCATCGAGGTGGTGGCG
CACAAGGACGACACCAGCAAGGAGCTCCTCGAATGGGGCTCCAGAGTCTCCGCCGCCAACTCCAGGCCGCCCAACCCGCA
GTAG

Alignment

ORF - retro_oglu_28 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.83 %
• Parental protein coverage: 93.56 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SAGEASLGRHLARRLVQVGVSDVFAVPGDFNLTLLDHLIAEPGLRLVGCCNELNAGYAADGYARARGVGA
          S.G.A.LG.HLARRLVQVGVSDVFAVPGDFNLTLLDHLIAEPGLR.VGCCNELNAGYAADGYARARGVGA
Retrocopy SSGDATLGGHLARRLVQVGVSDVFAVPGDFNLTLLDHLIAEPGLRVVGCCNELNAGYAADGYARARGVGA

Parental  CAVTFTVGGLSVLNAIAGAYSENLPVICIAGGPNSNDYGTNRILHHTIGLPDFSQELRCFQTVTCHQAVV
          CAVTFTVGGLSVLNAI.GAYSENLP.ICI.GGPNSNDYGTNRILHHTIGLPDFSQELRCFQ..TC.QAVV
Retrocopy CAVTFTVGGLSVLNAIGGAYSENLPLICIVGGPNSNDYGTNRILHHTIGLPDFSQELRCFQPLTCYQAVV

Parental  TNLEDAHEQIDTAIATALRESKPVYLSISCNLPGLPHPTFSRDPVPFFLAPRLSNKMGLEAAVEATVEFL
          .NL.DAH.QID.AI.TA.RESKPVY.S.SCNLP..PHPTFSRDPVP.FL.PRLSN...L.AA..AT..FL
Retrocopy NNLDDAHDQIDRAISTAIRESKPVYISVSCNLPAVPHPTFSRDPVPYFLSPRLSNQASLHAALDATLAFL

Parental  NKAVKPVLVGGPKLRVAKAGKAFVDLVDASGYAYAVMPSAKGLVPETHPHFIGTYWGAVSTAFCAEIVES
          .KAVKPVLV.GPKLRVAKAG.AFVDL.DASGYA.A.MPSAKGLVPET.P.FIGTYWGAVSTAFCAEIVES
Retrocopy DKAVKPVLVAGPKLRVAKAGGAFVDLADASGYAVAAMPSAKGLVPETLPRFIGTYWGAVSTAFCAEIVES

Parental  ADAYLFAGPIFNDYSSVGYSFLLKKDKAIIVQPERVIVGNGPAFGCVMMKEFLSELAKRVNKNTTAYENY
          ADAYLFAGPIFNDYSSVGYS.LLKK.KA..VQP.RV..GNGPAFGCVMM..FLSELAKRV.KNTTA..NY
Retrocopy ADAYLFAGPIFNDYSSVGYSCLLKKEKAVVVQPDRVTIGNGPAFGCVMMRDFLSELAKRVRKNTTAFDNY

Parental  KRIFVPEGQPLESEPNEPLRVNVLFKHVQKMLNSD--SAVIAETGDSWFNCQKLKLPEGCGYEFQMQYGS
          KRIFVPEGQ..E.E..E.LRVNVLFKH.Q.M.......AV.AETGDSWFNCQKL.LPEGCGYEFQMQYGS
Retrocopy KRIFVPEGQLPECEAGEALRVNVLFKHIQRMIGGAEIGAVMAETGDSWFNCQKLRLPEGCGYEFQMQYGS

Parental  IGWSVGALLGYAQGAKDKRVIACIGDGSFQVTAQDVSTMIRCAQNSIIFLINNGGYTIEVEIHDGPYNVI
          IGWSVGALLGYAQ.A..KRV.ACIGDGSFQVTAQDVSTM.RC.Q.SIIFLINNGGYTIEVEIHDGPYNVI
Retrocopy IGWSVGALLGYAQ-AVQKRVVACIGDGSFQVTAQDVSTMLRCGQRSIIFLINNGGYTIEVEIHDGPYNVI

Parental  KNWNYTGLVDAIHNGEGKCWTSKVKCEEELTEAIGMALGEKKDCLCFIEVIAHKDDTSKELLEWGSRVSA
          KNW.Y.GLV.AIHNGEG.CW...V.CEEEL..AI..A.G.K.D.LCFIEV.AHKDDTSKELLEWGSRVSA
Retrocopy KNWDYVGLVNAIHNGEGRCWATRVRCEEELEAAIATATGDKADSLCFIEVVAHKDDTSKELLEWGSRVSA

Parental  ANSRPPNPQ
          ANSRPPNPQ
Retrocopy ANSRPPNPQ

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Oryza glumaepatula was not studied using ChIP-Seq data.

EST

Oryza glumaepatula was not studied using EST data.

TSS

Oryza glumaepatula was not studied using FANTOM5 data.

Lab

retro_oglu_28 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza glumaepatula 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.

---

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,