RetrogeneDB ID: retro_olon_4

Retrocopy location

• Organism: Longstamen rice (Oryza longistaminata)
• Coordinates: AMDW01040231.1:1..1150(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: AMDW01040231.1_FG001
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: KN538848.1_FG012
• Aliases: None
• Description: None

Sequence

>retro_olon_4
AAAGGTGGCGGCGGCGACGTGCTGGAGGACGATCCGACGGGGAAGCTGAAGGTGTTCGTGTACGAGATGCCCCGAAAGTA
CAACCTGAACCTGCTGGCCAAGGACAGCCGGTGCCTGCAGCACATGTTCGCGGCGGAGATCTTCATGCACCAGTTCCTCC
TCTCCAGCCCCGTGCGCACCCTCGACCCGGAGGAGGCCGACTGGTTCTACACACCCGCCTACACCACCTGCGACCTCACC
CCGCAGGGCTTCCCGCTCCCCTTCCGCGCCCCGCGCATCATGCGCAGCGCCGTCCGCTACGTCGCCGCCACGTGGCCCTA
CTGGAACCGCACCGACGGCGCCGACCACTTCTTCCTCGCGCCGCACGACTTCGGCGCCTGCTTCCACTACCAGGAGGAGC
GCGCCATCGAGCGCGGCATCCTCCCGGTGCTCCGGCGCGCCACGCTGGTGCAGACGTTCGGCCAGCGCCACCACCCCTGC
CTCCAGCCGGGGTCGATCACCGTGCCGCCGTACGCCGATCCCCGCAAGATGGAGGCGCACCGGATCAGCCCGGCGACGCC
GCGCTCGATCTTCGTGTATTTTCGGGGGCTTTTCTACGACATGGGGAACGATCCCGAGGGCGGGTACTACGCCCGCGGCG
CGAGGGCGTCGGTGTGGGAGAACTTCAAGGACAACCCGCTGTTCGACATCTCGACGGAGCACCCGGCGACGTACTACGAG
GACATGCAGCGGGCCATCTTCTGCCTGTGCCCGCTGGGGTGGGCGCCGTGGAGCCCCCGGCTGGTGGAGGCGGTGGTGTT
CGGGTGCATCCCGGTGATCATCGCCGACGACATCGTGCTCCCCTTCGCGGACGCCATCCCGTGGGGGGAGATCAGCGTGT
TCGTGGCGGAGGAGGACGTGCCGAGGCTGGACACCATCCTGGCGTCCGTCCCGCTCGACGAGGTCATCCGGAAGCAGCGG
CTGCTGGCGTCCCCGGCGATGAAGCAGGCCGTGCTGTTCCACCAGCCGGCGAGGCCCGGCGACGCGTTCCACCAGATACT
CAACGGCCTCGCGCGCAAGCTGCCGCACCCCAAGGGCGTCTTCCTCGAGCCCGGCGAGAAGGGGATCGACTGGGATCAGG
GACTCGAGAACGACCTCAAGCCATGGTAG

Alignment

ORF - retro_olon_4 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.8 %
• Parental protein coverage: 92.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EGSAGDVLEDDPVGRLKVYVYELPTKYNKKMVAKDSRCLSHMFAAEIFMHRFLLSSAIRTLNPEEADWFY
          .G..GDVLEDDP.G.LKV.VYE.P.KYN....AKDSRCL.HMFAAEIFMH.FLLSS..RTL.PEEADWFY
Retrocopy KGGGGDVLEDDPTGKLKVFVYEMPRKYNLNLLAKDSRCLQHMFAAEIFMHQFLLSSPVRTLDPEEADWFY

Parental  TPVYTTCDLTPWGHPLPFKSPRIMRSAIQFISSHWPYWNRTEGADHFFVVPHDFGACFHYQEEKAIERGI
          TP.YTTCDLTP.G.PLPF..PRIMRSA.......WPYWNRT.GADHFF..PHDFGACFHYQEE.AIERGI
Retrocopy TPAYTTCDLTPQGFPLPFRAPRIMRSAVRYVAATWPYWNRTDGADHFFLAPHDFGACFHYQEERAIERGI

Parental  LPLLRRATLVQTFGQKDHVCLKEGSITIPPYAPPQKMKTHLVPPETPRSIFVYFRGLFYDTANDPEGGYY
          LP.LRRATLVQTFGQ..H.CL..GSIT.PPYA.P.KM..H...P.TPRSIFVYFRGLFYD..NDPEGGYY
Retrocopy LPVLRRATLVQTFGQRHHPCLQPGSITVPPYADPRKMEAHRISPATPRSIFVYFRGLFYDMGNDPEGGYY

Parental  ARGARASVWENFKNNPLFDISTDHPPTYYEDMQRSIFCLCPLGWAPWSPRLVEAVVFGCIPVIIADDIVL
          ARGARASVWENFK.NPLFDIST.HP.TYYEDMQR.IFCLCPLGWAPWSPRLVEAVVFGCIPVIIADDIVL
Retrocopy ARGARASVWENFKDNPLFDISTEHPATYYEDMQRAIFCLCPLGWAPWSPRLVEAVVFGCIPVIIADDIVL

Parental  PFADAIPWDEIGVFVAEDDVPKLDTILTSIPMDVILRKQRLLANPSMKQAMLFPQPAQPGDAFHQILNGL
          PFADAIPW.EI.VFVAE.DVP.LDTIL.S.P.D...RKQRLLA.P.MKQA.LF.QPA.PGDAFHQILNGL
Retrocopy PFADAIPWGEISVFVAEEDVPRLDTILASVPLDEVIRKQRLLASPAMKQAVLFHQPARPGDAFHQILNGL

Parental  GRKLPHPKSVYLDPGQKVLNWTQGPVGDLKPW
          .RKLPHPK.V.L.PG.K...W.QG...DLKPW
Retrocopy ARKLPHPKGVFLEPGEKGIDWDQGLENDLKPW

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Oryza longistaminata was not studied using ChIP-Seq data.

EST

Oryza longistaminata was not studied using EST data.

TSS

Oryza longistaminata was not studied using FANTOM5 data.

Lab

retro_olon_4 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza longistaminata 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza longistaminata	KN538848.1_FG012	1 retrocopy	retro_olon_4 ,
Oryza brachyantha	OB01G51480	1 retrocopy	retro_obra_20,
Solanum tuberosum	PGSC0003DMG400014472	1 retrocopy	retro_stub_120,
Solanum lycopersicum	Solyc12g042360.1	1 retrocopy	retro_slyc_19,