RetrogeneDB ID: retro_osat_24

Retrocopy location

• Organism: Rice subsp. japonica (Oryza sativa japonica)
• Coordinates: 11:21839988..21841863(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OS11G0578500
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OS11G0573800
• Aliases: None
• Description: None

Sequence

>retro_osat_24
ATGGAATGCAACAGAGAGGAGGCCTTCAGGGCCAGAGAAATTGCTGTAAAGAAGCTGGAAAATAGAGACTTTGTCGGCGC
CCGCAAGATCGCGATTAAAGCTCAAAGGCTTTTTCCTGAGCTTGAGAACATCTCCCAGCTGTTAATTATCTGTGAAGTTC
TTTCTTCAGCTGAGGCAAAGATCTCTGGAGAGTTGGATTGGTATGGTGTTCTTCAGGTGGATAAAATGGCAGACGAAACA
GTAATAAGAAGGCAATACAACATACTTTCGTATCGGCTTCATCCTGATAATAATACTCTGTTTGGTGCCGAAGCCGCATT
CAGGTTTGTTTCAGAAGCTCATGCAATATTGAGTGATCATGTGAAGAGGTCTCTGTATGACACCAAAAGACAGTGTGCTT
CAAGAGAAGTGGCCAAGGAGGCTACACAGCCACCAAACAAGACTGATTCAAACATAAGCAATGTGGCTGGATCCATGACA
CCATCTGCTTCTGTGCTTGTATTCTGGACAATATGTCCGCATTGTCAGAAGCGATTTCTGTACTACCAACGGAACTTTTT
GGCCCGCTGCAGTGATTGTGGTAAGAGGTTCTTCGCAATCAAACTGCATGAGCAGTCTGTTCCCTCGAGAATCCTATCAA
CTGCTGCAAAAAAGTCTCAGCTTTCAACGTCAGAAATGTTATCATTTCAACGAAGTAGTGTCCCCAATCAGCATCAACAA
GGTAAATGCTTGGTTACAAGAAGCGAGGCCATTCAATTTTCAGCAATGAAGCAAACTAAATCTCACATCTGCGCTTTTGA
CAATGATAAGCCTGGAACTTTGGTACCAAAGAGTTCTGATCTTAAGTCCATCTCAGTTAAGAATTTGACTAGAGAAAGTG
CACCTGCAGAGGAAAATGCTGCAGAATCATCCAGTCTTCAGATATTGGGTAAGAGAAAGCTTTATGTTACCTCTGACAGC
AGCCATGGTATGAACTCCAATATTAAGAGGCAAAGGAAGTATACTTGTCCATCCGATTCTGATTCGAGTAATGAGCAGAT
ATGTAATGATGATGTTGCTGTTCCTGATAATCAATCTACTGGACAGAATGTTCCCATCGAAGTGGACAGTGAAGAGGAAA
GAAATGCAAGACATGGAAGCAACCAACAAACTTGTAAGAAAAATGTTACTGATACTGCTTCTCAGAAGTCTGTCAATTCG
GTGATTGCCTACCCTTATCCAGACTTTGATTTTTGCAAGTCCAGAGATGCTGAAGAAACTGATGAATCCATAAAACAATA
TGGCTGGGCTGGTGACATGGCAGGTAAAGGCCTGGTGACAAGAAGTGACAGAGTTCAATTTTCAGAAATTAGCCAAGCTA
AATCTCATGTGCCTCCTGCTGACAACGATATACCCGGAACTTTGGTACCAAGGAGTCCTGATCCAAACTCCACCGCTGTG
CAGAATTTGACTGGAGAAAGTGTATCAGCAGAGACAAATGCTCCAGGATCATCCAGTCTTCAGATATTGGGTCGGAGAAA
GCTCTGTGATAGCTCTGACAGCAACCGTGCTATGAACTCTAATATTGAGAGGAAAATGAAGTATAATTCTCCATCTGATG
CTGATTGGAGTACTGAGCAAACATGTAATGATGATGTTGCTGTTACTGAGAATCAATTTGCCAAACAACATGTCCCCACC
GAAGTGGACAGTGAAGAGGAAGGAAATGAAAAACATGGAGACAATCAACAAAGTCATAGGAAAGATGATACTGATACTTC
TTCTCAGAATTCTGCCAATCCTGTGATTGCCTACTCTTCTACAGACTTCTTTGATTTTGACAAGTCCAGAGATGTGTCCC
AAATTGCGGTTGATCAGATCTGGGCAGTATATTAA

Alignment

ORF - retro_osat_24 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.63 %
• Parental protein coverage: 67.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MECNREEAFSAREIAVKKLENRDFVGARKIAIKAQRLFPELENISQLLTVCEVLSSAEAKISGELDWYGV
          MECNREEAF.AREIAVKKLENRDFVGARKIAIKAQRLFPELENISQLL..CEVLSSAEAKISGELDWYGV
Retrocopy MECNREEAFRAREIAVKKLENRDFVGARKIAIKAQRLFPELENISQLLIICEVLSSAEAKISGELDWYGV

Parental  LQVDKMADETVIRKQYNILSYRLHPDNNTLFGAEAAFRFVSEAHAVLSDHAKRSLYDTERQRASREVAKE
          LQVDKMADETVIR.QYNILSYRLHPDNNTLFGAEAAFRFVSEAHA.LSDH.KRSLYDT.RQ.ASREVAKE
Retrocopy LQVDKMADETVIRRQYNILSYRLHPDNNTLFGAEAAFRFVSEAHAILSDHVKRSLYDTKRQCASREVAKE

Parental  ATQPPNKTEANINNLAGSMPPSASVLVFWTICPHCQKQSLYYQRNFLARCNDCGK-FFAIKLREQSVPSR
          ATQPPNKT..NI.N.AGSM.PSASVLVFWTICPHCQK..LYYQRNFLARC.DCGK.FFAIKL.EQSVPSR
Retrocopy ATQPPNKTDSNISNVAGSMTPSASVLVFWTICPHCQKRFLYYQRNFLARCSDCGKRFFAIKLHEQSVPSR

Parental  ILSTAAKRSQLSPSEMFSFQRSSVPNQHQQGKCLVTRSEAIQFSAMKQTKSHICSSDNDKPGTLVPKSSD
          ILSTAAK.SQLS.SEM.SFQRSSVPNQHQQGKCLVTRSEAIQFSAMKQTKSHIC..DNDKPGTLVPKSSD
Retrocopy ILSTAAKKSQLSTSEMLSFQRSSVPNQHQQGKCLVTRSEAIQFSAMKQTKSHICAFDNDKPGTLVPKSSD

Parental  LNSISVKNLTRESAPAEENAAESSSFQILGKRKLYVTSDSSHGMNSNIKRQRKYICPSDSDSSNEQICND
          L.SISVKNLTRESAPAEENAAESSS.QILGKRKLYVTSDSSHGMNSNIKRQRKY.CPSDSDSSNEQICND
Retrocopy LKSISVKNLTRESAPAEENAAESSSLQILGKRKLYVTSDSSHGMNSNIKRQRKYTCPSDSDSSNEQICND

Parental  DVAVPDNQSTGQNVPIEVDSEEEGNARHGGNQQTCQKNVNDTAAQKYLNSVIAYPYPDFDFGKSRDTEET
          DVAVPDNQSTGQNVPIEVDSEEE.NARHG.NQQTC.KNV.DTA.QK..NSVIAYPYPDFDF.KSRD.EET
Retrocopy DVAVPDNQSTGQNVPIEVDSEEERNARHGSNQQTCKKNVTDTASQKSVNSVIAYPYPDFDFCKSRDAEET

Parental  DESIKQYGWAGDMEGKGLVTRSDRVQFSEISQAKSHVPPADNDMPGTLVPRSPDPNSIAVQNLTGESVSA
          DESIKQYGWAGDM.GKGLVTRSDRVQFSEISQAKSHVPPADND.PGTLVPRSPDPNS.AVQNLTGESVSA
Retrocopy DESIKQYGWAGDMAGKGLVTRSDRVQFSEISQAKSHVPPADNDIPGTLVPRSPDPNSTAVQNLTGESVSA

Parental  GTNAPGSSSLQILGRRKLCDSSDSSRAMNSNIERKRKYNSPSDADWSNEQICNDDVAVTENQFAKQHVPI
          .TNAPGSSSLQILGRRKLCDSSDS.RAMNSNIERK.KYNSPSDADWS.EQ.CNDDVAVTENQFAKQHVP.
Retrocopy ETNAPGSSSLQILGRRKLCDSSDSNRAMNSNIERKMKYNSPSDADWSTEQTCNDDVAVTENQFAKQHVPT

Parental  EVDSEEEGNEKHGDNQQSHRKDDTDTSSQNSANPVIAYSSPDFFNFDKSRDVSQIAVDQIWAVY
          EVDSEEEGNEKHGDNQQSHRKDDTDTSSQNSANPVIAYSS.DFF.FDKSRDVSQIAVDQIWAVY
Retrocopy EVDSEEEGNEKHGDNQQSHRKDDTDTSSQNSANPVIAYSSTDFFDFDKSRDVSQIAVDQIWAVY

Legend:

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

Expression

RNA-Seq

Oryza sativa japonica was not studied using RNA-Seq expression data.

ChIP-Seq

Oryza sativa japonica was not studied using ChIP-Seq data.

EST

Oryza sativa japonica was not studied using EST data.

TSS

Oryza sativa japonica was not studied using FANTOM5 data.

Lab

retro_osat_24 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza sativa japonica 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 sativa japonica	OS11G0573800	1 retrocopy	retro_osat_24 ,