RetrogeneDB ID: retro_osat_1

Retrocopy location

• Organism: Rice subsp. japonica (Oryza sativa japonica)
• Coordinates: 6:7982026..7983859(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OS06G0254200
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OS01G0718700
• Aliases: None
• Description: None

Sequence

>retro_osat_1
ATGACAAGACAAGGCAGCACATCGGTGACAATACTACCAGTAACGATGAGCCCCGCCATGGCCGCTAGAAGCGAGCTTCT
CCGGCCGGCATTTGGTGAAGCATCTCCTTCGCTAGGACGGTTTGTCATTAACCCTCACAGCTGCAGCTACAGGTGGTGGC
ACATGTTCCTGATCATGCTGGTGTTGTACTCGGCATGGGCATCGCCGTTCGAGCTGTCCATGGAGAAGGCAGCCTCCATT
GCTCTTGTTGTCACAGACCTGGTGGTCGATGTCTTCTTCGCCATTGACATTGCCTTATCCTTCTTCGTCGCATACCGTGA
CACCTCCACCGGCCTCCTCATAACTGACCGCAGGAAGATCACAATGAGGTACCTGAAACGGCCGTGTTTCGCTCTGGATG
TGGCCTCGACGATTCCTTTACAAATAATCTACCAGCTTGTGACTGGCAAAAGACAAGGACTGTGGGGGCTCCTCAATCTT
CTCCGTCTTTGGCGACTACGGCGCGTCAGCAAGCTCTTTGCGAGGGTGGAGAAGGACATCAGATTCAACTATTTGTGGAC
CAGGCTTATCAAGCTCCTTTGTGTGACACTGTTTGCGCTGCATTTTGCCGCTTGCATCTACCTGTGGATGGCATTCAACT
ACAAGATCAAGGAGCTTACATGGATAGGCAGCCAGATCCATAGCTTTGAGGACCGAAGCGTGTGGTTTTGCTACACCTGT
GCAGTGTACTGGTCCATCACCACGCTTGCCACGGTCGGCTACGGTGACCTACATGCCACCAACATTGGCGAGATGCTTTT
CAGCATAGCCTTCATGCTTTTCAACATGGGCCTCACATCCTACATCATCGGCAACATCACCAACCTCGTTGTCCGTGAAA
CCTCCAACACCTTCAAGATGAGGGACATGGTGCAGCGGGTGTCGGAGTTCGGGAGAATGAACCGGCTGCCAGAGGCGATG
AGGGAGCAGATGTTGGCCAGCGTGCAGCTCAGGTTCAGGACAGATGAGCAGCTGCAGCAGGAGATGTTGTCAGAGCTGCC
CAAGGCTGTGCGGTCGGGCGTCATGAAGCACATGTTCAAGAGTGCTATCGAGAGCTGCTACCTATTCCAGGGAGTCTCCG
ACAGCCTCATTGTGCAGCTGGTCGCGGAGATGAAAGCAGAATTCTTTCCCCCCAAGGCTAATGTTATCCTAGAGAATGAG
ACCTCGACGGACTGTTATATCATCATCTCTGGCGAAGTGGAGGCATTGACAACCCTTGCAGATGGGACAGAGAAGCATGT
GAAGAGAATAGGACCTCGGGGCATGGCAGGGGAAATCGGGGTGATGTTCAGCATTCCGCAACCATTCACCATCCGGAGCA
GGAGACTCACCCAGGTTGTCCGCATAAGCCATATCCATCTGCTTCAGGCTGTCCGGCCTAACACCGCAGATGGGTACATC
GTGTTCTCCAATTTTATTCAGTACCTTGAGTCTCTGAAGGTGCAAACAAAGGATGTGGCTTTTGTCAGCGATCATCTTTG
GAATGGAAACTCAATGGTTTTGAGAAGGGCAACCGAGGTTGCTGTAGATGAATCAAAAGAGGCCGCTCACAAAATGTTAC
CATGCAAAGAACCCAAACGGGTTGTTATTCATGAGCAACTTCCCAACGCGACTAGCACAGCACTGCATCCTTCGCCGGGG
AAGCTCGTCTTACTCCCAGATTCGATGCAAGAACTGATGAAACTTTCAGAAAAGAAATTTGGGAAGGCCGTGAGAGGGAT
CCTCACTGTGGAAGGAGCCGAGGTTGAGGACATTGAAGTGATAAGAGATGGCGATCACCTGTTATTTAGTTAG

Alignment

ORF - retro_osat_1 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.09 %
• Parental protein coverage: 97.32 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RWWQKFLIVLVLYTAWASPFELAMEKSASAALAVTELVVDAFFAVDIAVSFFVAYRDASTGLLVTDRKKI
          RWW..FLI.LVLY.AWASPFEL.MEK.AS.AL.VT.LVVD.FFA.DIA.SFFVAYRD.STGLL.TDR.KI
Retrocopy RWWHMFLIMLVLYSAWASPFELSMEKAASIALVVTDLVVDVFFAIDIALSFFVAYRDTSTGLLITDRRKI

Parental  ATRHLARPCLALDVASTIPLQMIYRIVSGKRQALYGLLNLLRLWRLRRVSKLFARLEKDIRFSYLWTRLI
          ..R.L.RPC.ALDVASTIPLQ.IY..V.GKRQ.L.GLLNLLRLWRLRRVSKLFAR.EKDIRF.YLWTRLI
Retrocopy TMRYLKRPCFALDVASTIPLQIIYQLVTGKRQGLWGLLNLLRLWRLRRVSKLFARVEKDIRFNYLWTRLI

Parental  KLLYVTLFAVHFASCIYLWMAFHHKAKELTWIGSQFHGFEDRSVWFCYTCAVYWSITTLATVGYGDLHAA
          KLL.VTLFA.HFA.CIYLWMAF..K.KELTWIGSQ.H.FEDRSVWFCYTCAVYWSITTLATVGYGDLHA.
Retrocopy KLLCVTLFALHFAACIYLWMAFNYKIKELTWIGSQIHSFEDRSVWFCYTCAVYWSITTLATVGYGDLHAT

Parental  NTGEMLFSIAFMLFNMGLTSYIIGNITNLVVHETTNTFKMRDMVQRTSVFGRTNRLPVAMREQMMESLQL
          N.GEMLFSIAFMLFNMGLTSYIIGNITNLVV.ET.NTFKMRDMVQR.S.FGR.NRLP.AMREQM..S.QL
Retrocopy NIGEMLFSIAFMLFNMGLTSYIIGNITNLVVRETSNTFKMRDMVQRVSEFGRMNRLPEAMREQMLASVQL

Parental  RFRAEEQLQQEMLSELPKAVRSGIAQHMFRGAVQSCYLFQGVSDKLVLPLVAEMKAESFPPKADIILENE
          RFR..EQLQQEMLSELPKAVRSG...HMF..A..SCYLFQGVSD.L...LVAEMKAE.FPPKA..ILENE
Retrocopy RFRTDEQLQQEMLSELPKAVRSGVMKHMFKSAIESCYLFQGVSDSLIVQLVAEMKAEFFPPKANVILENE

Parental  ASTDCYIIVSGEV
          .STDCYII.SGEV
Retrocopy TSTDCYIIISGEV

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_1 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA004342	1 retrocopy	retro_oind_32,
Oryza brachyantha	OB01G37960	1 retrocopy	retro_obra_2,
Oryza barthii	OBART01G29050	1 retrocopy	retro_obar_20,
Oryza glumaepatula	OGLUM01G33050	1 retrocopy	retro_oglu_27,
Oryza nivara	ONIVA01G33130	1 retrocopy	retro_oniv_11,
Oryza rufipogon	ORUFI01G32100	1 retrocopy	retro_oruf_17,
Oryza sativa japonica	OS01G0718700	1 retrocopy	retro_osat_1 ,
Setaria italica	Si003861m.g	1 retrocopy	retro_sita_40,