RetrogeneDB ID: retro_ogla_22

Retrocopy location

• Organism: African rice (Oryza glaberrima)
• Coordinates: 7:21599439..21601203(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ORGLA07G0217100
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ORGLA05G0173200
• Aliases: None
• Description: None

Sequence

>retro_ogla_22
TTAATGGAGAGCAACGGCGGAGGAGGAGGATCTCCCAAGGAGGCAGCGGTGGTGGTGCCGTCCTCCGGCGACGCCACACT
GGGCGGGCACCTGGCGCGGCGCCTCGTGCAGGTGGGCGTGAGCGACGTGTTCGCCGTGCCGGGGGACTTCAACCTGACGC
TTCTGGACCACCTGATCGCCGAGCCCGGGCTCCGCGTGGTGGGCTGCTGCAACGAGCTGAACGCCGGATACGCGGCCGAC
GGGTACGCGCGGGCCCGTGGCGTGGGCGCCTGCGCCGTGACCTTCACCGTGGGCGGGCTGAGCGTGCTGAACGCCATCGG
CGGCGCGTACAGCGAGAACCTGCCGCTGATCTGCATCGTGGGGGGCCCAAACTCCAACGACTACGGCACCAACCGCATCC
TCCACCACACCATCGGCCTCCCGGACTTCTCCCAGGAGCTCCGCTGCTTCCAGCCCCTCACCTGCTACCAGGCCGTCGTC
AACAACCTCGACGACGCCCACGACCAGATCGACCGCGCCATCTCCACCGCCATCAGGGAGAGCAAGCCCGTCTACATCAG
CGTCAGCTGCAACCTCCCCGCCGTCCCCCACCCCACCTTCTCCCGCGACCCGGTGCCCTACTTCCTCTCCCCGAGGCTCT
CCAACCAGGCCAGCCTCCACGCCGCGCTCGACGCCACCCTCGCCTTCCTCGACAAGGCCGTCAAGCCCGTCCTCGTCGCG
GGGCCCAAGCTCCGCGTCGCCAAGGCCGGAGGGGCCTTCGTGGACCTCGCCGACGCCAGCGGCTACGCGGTGGCCGCCAT
GCCGTCCGCCAAGGGGCTGGTGCCGGAGACGCTGCCGCGCTTCATCGGGACCTACTGGGGCGCGGTCAGCACGGCCTTCT
GCGCGGAGATCGTGGAGTCCGCGGACGCCTACCTGTTCGCGGGGCCCATCTTCAACGACTACAGCTCCGTGGGGTACTCG
TGCCTGCTGAAGAAGGAGAAGGCGGTGGTGGTGCAGCCCGACCGCGTGACCATCGGCAATGGCCCCGCGTTCGGGTGCGT
GATGATGAGGGACTTCCTGTCGGAGCTGGCCAAGCGCGTCCGGAAGAACACGACGGCGTTCGACAACTACAAGAGGATCT
TCGTGCCGGAGGGGCAGCTGCCGGAGTGCGAGGCCGGGGAGGCGCTGCGGGTGAACGTGCTGTTCAAGCACATACAGAGG
ATGATCGGTGGCGCGGAGATCGGGGCGGTGATGGCGGAGACGGGGGACTCGTGGTTCAACTGCCAGAAGCTGCGGCTGCC
CGAGGGTTGCGGGTACGAGTTCCAGATGCAGTACGGCTCCATCGGGTGGTCGGTGGGGGCGCTGCTGGGCTACGCGCAGG
CTGTCCAAAAACGGGTGGTGGCTTGCATCGGCGACGGCAGCTTCCAGGTGACGGCGCAGGACGTGTCGACGATGCTGCGT
TGCGGGCAGCGGAGCATCATCTTCCTCATCAACAACGGCGGGTACACCATCGAGGTGGAGATCCACGACGGGCCGTACAA
CGTGATCAAGAACTGGGACTACGTGGGCCTCGTCAACGCCATCCACAACGGCGAGGGGCGGTGCTGGGCCACCCGGGTGC
GGTGCGAGGAGGAGCTGGAGGCGGCCATCGCGACGGCCACGGGGGACAAGGCGGACAGCCTCTGCTTCATCGAGGTGGTG
GCGCACAAGGACGACACCAGCAAGGAGCTCCTCGAATGGGGCTCCAGAGTCTCCGCCGCCAACTCCAGGCCGCCCAACCC
GCAG

Alignment

ORF - retro_ogla_22 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.2 %
• Parental protein coverage: 94.06 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VTSAAGATLGRHLARRLVQIGATDVFAVPGDFNLTLLDYLIAEPGLKLIGCCNELNAGYAADGYARARGV
          V.S...ATLG.HLARRLVQ.G..DVFAVPGDFNLTLLD.LIAEPGL...GCCNELNAGYAADGYARARGV
Retrocopy VPSSGDATLGGHLARRLVQVGVSDVFAVPGDFNLTLLDHLIAEPGLRVVGCCNELNAGYAADGYARARGV

Parental  GACAVTFTVGGLSVLNAIAGAYSENLPVICIVGGPNSNDYGTNRILHHTIGLPDFSQELRCFQTITCYQA
          GACAVTFTVGGLSVLNAI.GAYSENLP.ICIVGGPNSNDYGTNRILHHTIGLPDFSQELRCFQ..TCYQA
Retrocopy GACAVTFTVGGLSVLNAIGGAYSENLPLICIVGGPNSNDYGTNRILHHTIGLPDFSQELRCFQPLTCYQA

Parental  VINNLDDAHEQIDTAIATALRESKPVYISVGCNLAGLSHPTFSREPVPLFISPRLSNKANLEYAVEAAAD
          V.NNLDDAH.QID.AI.TA.RESKPVYISV.CNL....HPTFSR.PVP.F.SPRLSN.A.L..A..A...
Retrocopy VVNNLDDAHDQIDRAISTAIRESKPVYISVSCNLPAVPHPTFSRDPVPYFLSPRLSNQASLHAALDATLA

Parental  FLNKAVKPVMVGGPKIRVAKAKKAFAGIAESSGYPFAVMPSAKGLVPEHHPRFIGTYWGAVSTTFCAEIV
          FL.KAVKPV.V.GPK.RVAKA..AF...A..SGY..A.MPSAKGLVPE..PRFIGTYWGAVST.FCAEIV
Retrocopy FLDKAVKPVLVAGPKLRVAKAGGAFVDLADASGYAVAAMPSAKGLVPETLPRFIGTYWGAVSTAFCAEIV

Parental  ESADAYLFAGPIFNDYSSVGYSLLLKREKAVIVQPDRVVVGNGPAFGCILMTEFLDALAKRLDRNTTAYD
          ESADAYLFAGPIFNDYSSVGYS.LLK.EKAV.VQPDRV..GNGPAFGC..M..FL..LAKR...NTTA.D
Retrocopy ESADAYLFAGPIFNDYSSVGYSCLLKKEKAVVVQPDRVTIGNGPAFGCVMMRDFLSELAKRVRKNTTAFD

Parental  NYRRIFIPDREPPNGQPDEPLRVNILFKHIKEMLSGDT--AVIAETGDSWFNCQKLRLPEGCGYEFQMQY
          NY.RIF.P....P.....E.LRVN.LFKHI..M..G....AV.AETGDSWFNCQKLRLPEGCGYEFQMQY
Retrocopy NYKRIFVPEGQLPECEAGEALRVNVLFKHIQRMIGGAEIGAVMAETGDSWFNCQKLRLPEGCGYEFQMQY

Parental  GSIGWSVGATLGYAQAAKDKRVISCIGDGSFQQMTAQDVSTMLRCGQKSIIFLINNGGYTIEVEIHDGPY
          GSIGWSVGA.LGYAQA...KRV..CIGDGSF.Q.TAQDVSTMLRCGQ.SIIFLINNGGYTIEVEIHDGPY
Retrocopy GSIGWSVGALLGYAQAVQ-KRVVACIGDGSF-QVTAQDVSTMLRCGQRSIIFLINNGGYTIEVEIHDGPY

Parental  NVIKNWDYTGLIDAIHNSDGNCWTKKVRTEEELIEAIATATGAKKDCLCFIEIIVHKDDTSKELLEWGSR
          NVIKNWDY.GL..AIHN..G.CW...VR.EEEL..AIATATG.K.D.LCFIE...HKDDTSKELLEWGSR
Retrocopy NVIKNWDYVGLVNAIHNGEGRCWATRVRCEEELEAAIATATGDKADSLCFIEVVAHKDDTSKELLEWGSR

Parental  VSAANSRPPNPQ
          VSAANSRPPNPQ
Retrocopy VSAANSRPPNPQ

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Oryza glaberrima was not studied using ChIP-Seq data.

EST

Oryza glaberrima was not studied using EST data.

TSS

Oryza glaberrima was not studied using FANTOM5 data.

Lab

retro_ogla_22 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza glaberrima 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 glaberrima	ORGLA05G0173200	1 retrocopy	retro_ogla_22 ,