RetrogeneDB ID: retro_olon_3

Retrocopy location

• Organism: Longstamen rice (Oryza longistaminata)
• Coordinates: KN542618.1:8357..9719(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: KN542618.1_FG003
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: KN538917.1_FG011
• Aliases: None
• Description: None

Sequence

>retro_olon_3
ATGGCGTCGGTGGCGGTGCCGGAGTGGCTGAACAAGGGCGACAATGCGTGGCAGATGCTCTCCGCCACGCTCGTCGCCCT
GCAGGGCTTCCCCGGTCTCGCCCTCTTCTACGCCGGTGCCGTCCCGCGCAAGTGGGCTCTCACCTCCGCATTCATGGCGC
TCTACGCCATGGCCGCCACCATGCCGTGCTGGGCGCTCTGGGCGCACAACATGGCCTTCGGCCACCGCCTCCTCCCTTTC
GTCGGCCGCCCCGCCCCGGCGCTCGCCCAGGACTACATGCTCACCCAGGCGCTGCTCCCCTCCACCCTCCACCTCCGCTC
CAACGGCGAGGTTGAGACGGCCGCCGTGGCGCCGCTGTACCCGTCGGCGAGCATGGTGTTCTTCCAGTGGGCCTTCGCCG
GCGTCACCGTGGGGCTGGTCGCCGGCGCCGTGCTCGGCCGCATGAGCGTCAAGGCGTGGATGGCGTTCGTGCCGCTGTGG
ACGACGCTGTCCTACACGGTGGGGGCGTACAGCATTTGGGGCGGAGGCTTCCTCTTCCACTGGGGCGTCATAGACTACTC
CGGCGGCTACGTCGTGCACCTCGCCGCTGGCGTCTCCGGCTACACGGCCGCGTACTGGGTGGGACCGAGGAGGAAGGAGG
AGGCGGGTGGTGGCAACCTGGTGGTGATGGTGGCCGGCGCGGGCATCCTGTGGATGGGGTGGACCGGCTTCAACGGCGGC
GACCCCTTCTCCGCCAACACCGACTCGTCGGTGGCGGTGCTCAACACGCACATCTGCGCCACCACCAGCATCCTCGCTTG
GATTTGCTGCGACGTCGCCGTCCGGGGGAGGCCGTCGGTGGTTGGCGCGGTGCAGGGCATGATCACCGGCCTGGTGTGCA
TCACCCCGGCGGCAGGGCTGGTGCAGGGGTGGGCAGCTCTGCTAATGGGCGTCGCGTCGGGGACACTGCCATGCTACACC
ATGAACGCCGCCATGTCGTTCAAGGTAGACGACACGCTGGGCATCCTGCACACCCACGCGGTGTCCGGCGTTCTGGGCGG
CGTCCTCACCGGCGTCTTCGCGCACCCTACTCTCTGCGACATGTTCCTTCCGGTGACTGGCTCCAGGGGCCTCGTCTACG
GCGTCCGCGCCGGCGGAGTGCAGGTGTTGAAGCAGGTCGCCGCCGCATTGTTCGTTGCCGCATGGAACGTGGCCGCCACG
TCCATCATCTTGGTCGTCGTCAGGGCGTTCGTGCCGCTGAGGATGACGGAAGATGAGCTGCTCGCCGGAGACATTGCCGT
TCATGGGGAACAAGCTTATTATTTTTCGAGTGGCACCAATTGTAGTTTAAGCCATGAGACCATTGAGGTCGGAAATTTAT
AA

Alignment

ORF - retro_olon_3 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.84 %
• Parental protein coverage: 66.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PDWLNKGDNAWQMTSATLVGLQSMPGLVILYGSIVKKKWAINSAFMALYAFAAVWICWVVWAYNMSFGDR
          P.WLNKGDNAWQM.SATLV.LQ..PGL...Y...V..KWA..SAFMALYA.AA...CW..WA.NM.FG.R
Retrocopy PEWLNKGDNAWQMLSATLVALQGFPGLALFYAGAVPRKWALTSAFMALYAMAATMPCWALWAHNMAFGHR

Parental  LLPFWGKARPALGQSFLVAQSELTATAIRYHNGSAEAPMLKPLYPVATMVYFQCMFASITVIILAGSLLG
          LLPF.G...PAL.Q.....Q..L..T.....NG..E.....PLYP.A.MV.FQ..FA..TV...AG..LG
Retrocopy LLPFVGRPAPALAQDYMLTQALLPSTLHLRSNGEVETAAVAPLYPSASMVFFQWAFAGVTVGLVAGAVLG

Parental  RMNIKAWMAFVPLWITFSYTVCAFSLWGGGFLFQWGVIDYSGGYVIHLSSGIAGLTAAYWVGPRSASDRE
          RM..KAWMAFVPLW.T.SYTV.A.S.WGGGFLF.WGVIDYSGGYV.HL..G..G.TAAYWVGPR.....E
Retrocopy RMSVKAWMAFVPLWTTLSYTVGAYSIWGGGFLFHWGVIDYSGGYVVHLAAGVSGYTAAYWVGPRR---KE

Parental  RFPPNNILLVLAGAGLLWLGWTGFNGGDPYSANIDSSMAVLNTHICASTSLLVWTILDVFFFGKPSVIGA
          .....N.....AGAG.LW.GWTGFNGGDP.SAN.DSS.AVLNTHICA.TS.L.W...DV...G.PSV.GA
Retrocopy EAGGGNLVVMVAGAGILWMGWTGFNGGDPFSANTDSSVAVLNTHICATTSILAWICCDVAVRGRPSVVGA

Parental  VQGMITGLVCITPGAGLVQGWAAIVMGILSGSIPWYTM
          VQGMITGLVCITP.AGLVQGWAA..MG..SG..P.YTM
Retrocopy VQGMITGLVCITPAAGLVQGWAALLMGVASGTLPCYTM

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_3 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryza longistaminata	KN538917.1_FG011	1 retrocopy	retro_olon_3 ,