RetrogeneDB ID: retro_olon_14

Retrocopy location

• Organism: Longstamen rice (Oryza longistaminata)
• Coordinates: KN538884.1:189577..190660(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: KN538884.1_FG003
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: KN538775.1_FG004
• Aliases: None
• Description: None

Sequence

>retro_olon_14
ATGTCCGGCGGCGGCGCCACCTCGGAGTGCCTCTTCGGCTTCATCGCCTCCGCGCTAGCCGAGTTCGTCGGCGAGGAGGA
AGAAGAAGGCGGCCTCGACGGCGGCGAGAGGGAGCTTGGGTTCACCTTCTCCTTCCCCGTGCACCAAACCTCCATCGCGT
CGGGGACGCTCATCCGGTGGACGAAGGCGTTCGCCGTCGACGACGCGATCGGCGAGGACGTCGTGGCGGCGCTGCAGGCG
GCCATGTCGGAGCGGGGGCTCGACATGCGCGTGTCGGCGCTCATCAACGACACCGTCGGGACGCTCGCCGCGGGCAGCTA
CTACGACGAGGACGTCGTGGCCGCCGTCATCCTCGGCACCGGCACGAACGCCGCCTACGTCGAGGACGCCACCGCCATCG
CCAAGCTACACCCATCGCAGCTGCCAGCATCGAACACCATGGTGATCAACACCGAGTGGGGCAGCTTCGCCTCGCCGTGC
CTCCCATTGACGGAGTTCGACGAAGCACTCGATCAGGAGAGCCTCAACCCCGGCGAGCAGACCTACGAGAAGCTCATCTC
CGGGATGTACCTCGGCGAGATCGTCAGGAGGGTCCTCCTCAAGATCTCCTCCCGGTGCCCCTCCCTCCTCGGCGGCGCCG
GCGAGCTCGCGACGCCGTTCGTCCTCAAGACACCCGACGTGTCCGCGATGCACCACGACGAGACGCCCGACCTGAGCATC
GTCGGCGAGAAGCTGGAACGCACGCTGGGCATCCGCGGCACGTCGCCGGAGGCGAGGAGGATGGTCGTCGAGGTGTGCGA
CATCGTCGCCACGAGGGCCGCCCGGCTGGCCGCGGCGGGGATCGTCGGGATCCTGAAGAAGATCGGGAGGGTCGACGGCG
GCGAGGGGCGGAGGAGGAGGTCGGTGGTCGCCGTGGACGGCGGCCTGTTCGAGCACTACGGCAAGTTCCGGCGGTGCATG
GAGAGCGCGGTGAGGGAGCTGCTCGGAGAGGCGGCGGCGGAGAGGGTGGTCGTCAAGCTCGCCAGCGACGGCTCCGGGCT
CGGCGCCGCCCTGGTTGCAGCTGCTCACTCGCAGAGAGCATAA

Alignment

ORF - retro_olon_14 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.84 %
• Parental protein coverage: 81.69 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TSMELFDFIAAELESFVKTEGEDFHLPEGRQRELGFTFSFPVHQTSISSGTLIKWTKGFSINGTVGEDVV
          TS..LF.FIA..L..FV..E.E...L..G..RELGFTFSFPVHQTSI.SGTLI.WTK.F......GEDVV
Retrocopy TSECLFGFIASALAEFVGEEEEEGGL-DGGERELGFTFSFPVHQTSIASGTLIRWTKAFAVDDAIGEDVV

Parental  AELSRAMERQGLDMKVTALVNDTVGTLAGGRYVDNDVVAAVILGTGTNAAYVEHANAIPK-WTGLLPRSG
          A.L..AM...GLDM.V.AL.NDTVGTLA.G.Y.D.DVVAAVILGTGTNAAYVE.A.AI.K.....LP.S.
Retrocopy AALQAAMSERGLDMRVSALINDTVGTLAAGSYYDEDVVAAVILGTGTNAAYVEDATAIAKLHPSQLPASN

Parental  NMVINMEWGNFKSERLPRSDYDNALDFESLNPGEQIYEKMISGMYLGEIVRRILLKLAHDA-SLFGDVVP
          .MVIN.EWG.F.S..LP....D.ALD.ESLNPGEQ.YEK.ISGMYLGEIVRR.LLK......SL.G....
Retrocopy TMVINTEWGSFASPCLPLTEFDEALDQESLNPGEQTYEKLISGMYLGEIVRRVLLKISSRCPSLLGGA--

Parental  TKLEQRFILRTPDMSAMHHDTSHDLKHLGAKLKDILGVADTSLEARYITLHVCDLVAERGARLAAAGIYG
          ..L...F.L.TPD.SAMHHD...DL...G.KL...LG...TS.EAR.....VCD.VA.R.ARLAAAGI.G
Retrocopy GELATPFVLKTPDVSAMHHDETPDLSIVGEKLERTLGIRGTSPEARRMVVEVCDIVATRAARLAAAGIVG

Parental  ILKKLGRDKVPSDGSQKQRTVIALDGGLYEHYKKFRTCLEATLADLLGEEAASSVVVKLANDGSGIGAAL
          ILKK.GR..V........R.V.A.DGGL.EHY.KFR.C.E.....LLGE.AA..VVVKLA.DGSG.GAAL
Retrocopy ILKKIGR--VDGGEGRRRRSVVAVDGGLFEHYGKFRRCMESAVRELLGEAAAERVVVKLASDGSGLGAAL

Parental  LAASHSQYA
          .AA.HSQ.A
Retrocopy VAAAHSQRA

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_14 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.

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza longistaminata	KN538775.1_FG004	1 retrocopy	retro_olon_14 ,
Leersia perrieri	LPERR01G26100	1 retrocopy	retro_lper_19,
Oryza sativa japonica	OS01G0742500	1 retrocopy	retro_osat_8,