RetrogeneDB ID: retro_ogla_45

Retrocopy location

• Organism: African rice (Oryza glaberrima)
• Coordinates: 12:4347415..4348822(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ORGLA12G0053900
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ORGLA11G0052300
• Aliases: None
• Description: None

Sequence

>retro_ogla_45
ATGGTTCAGATCGAGCCGCTCGAGGTGTCACTGGAGGCCGGCAACCAGGCGGACTCGGCGTTGCTCGACGACGACGGGCG
GCCGCGCCGCACCGGCACGTTCTGGACGGCGAGCGCGCACATCATCACCGCCGTGATCGGGTCCGGGGTGCTGTCTCTGC
CGTGGGCGACGGCGCAGCTCGGGTGGGTCGCCGGGCCCGCCGTGATGGTGGTGTTCGGCGGCGTCACCTACTTCACCGCC
ACGCTCCAGGCCGAGTGCTACCGCACCGGCGACGAGGAGACCGGCGCCCGCAACTACACCTACATCGGCGCCGTGCGCGC
CATCCTCGGCGGCGCCAACGCCAAGCTCTGCGGCATCATCCAGTACGCCAACCTCGTCGGCACCGCCATCGGCTACACCA
TCGCCGCCTCCATCAGCATGCAGGCCATCAAGAGGGCGGGCTGCTTCCACGCCAATGGCCACAACGTCCCGTGCCACATC
TCGAGCACCCCGTACATGCTCATCTTCGGCGCCTTCGAGATCGTCTTCTCGCAGATCCCCGACTTCCACGAGATCTGGTG
GCTGTCCATCGTCGCCGCCGTCATGTCCTTCACCTACTCCGGCGTCGGCCTCGGCCTCGGCATCGCCCAGACCGTCGCCG
ACGGCGGGTTCCGCGGCACGATCGCCGGCGTCACCAACGTCACCGCCACGCAGAAGGCGTGGCGGTCGCTGCAGGCGCTG
GGCAACATCGCCTTCGCGTTCGCCTTCTCCAACGTGTACACCGAGATCCAGGACACGATCAAGGCGCCGCCGCCGTCGGA
GGCGAAGGTGATGAAGCAGGCGTCGCTGCTGAGCATCGTGGCGACGTCGGTGTTCTACGCGCTGTGCGGGTGGATGGGCT
ACGCGGCGTTCGGCAACGCGGCGCCGGACAACCTCCTCACCGGATTCGGCTTCTTCGAGCCGTTCTGGCTCGTCGACGCC
GCCAACGTCGCCATCGCCGTGCACCTCATCGGCGCCTACCAGGTGTACTGCCAGCCGGTCTTCGCCTTCGTCGAGCGCAA
GGCGTCGCGCCGGTGGCCCGACAGCGGCTTCGTCAACAGCGAGCTCCGGGTGGGCCCCTTCGCCATCAGCGCGTTCCGGC
TGGCGTGGCGCTCGGTGTTCGTCTGCTTCACCACCGTGGTCGCCATGGCGCTGCCCTTCTTCGGCGTCATCGTCGGCCTC
CTCGGCGCCATATCCTTCTGGCCGCTCACCGTCTACCTCCCCACGGAGATGTACATCGCGCAGCGCGGCGTGCGGCGCGG
CAGCGCACTGTGGATCGGGCTCAGGGCGCTCGCCGTCGCCGGCTTCATCGTGTCGGCCGCCGCCACCACGGGCGCCGTCG
CCAACTTCGTCGGCGACTTCATGAAATTCCGTCCCTTCAGTGGATAG

Alignment

ORF - retro_ogla_45 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.16 %
• Parental protein coverage: 94.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DDDGRARRTGTVWTASAHIITAVIGSGVLSLAWAIAQLGWVAGPAVMLLFAFVIYYTSTLLAECYRSGDP
          DDDGR.RRTGT.WTASAHIITAVIGSGVLSL.WA.AQLGWVAGPAVM..F..V.Y.T.TL.AECYR.GD.
Retrocopy DDDGRPRRTGTFWTASAHIITAVIGSGVLSLPWATAQLGWVAGPAVMVVFGGVTYFTATLQAECYRTGDE

Parental  CTGKRNYTYMDAVRANLGGAKVRLCGVIQYANLFGVAIGYTIAASISMLAIKRADCFHEKGHKNPCRSSS
          .TG.RNYTY..AVRA.LGGA...LCG.IQYANL.G.AIGYTIAASISM.AIKRA.CFH..GH..PC..SS
Retrocopy ETGARNYTYIGAVRAILGGANAKLCGIIQYANLVGTAIGYTIAASISMQAIKRAGCFHANGHNVPCHISS

Parental  NPYMILFGVVQIVFSQIPDFDQIWWLSIVAAIMSFTYSTIGLSLGIAQTVANGGFMGSLTGISVGAGVTS
          .PYM..FG...IVFSQIPDF..IWWLSIVAA.MSFTYS..GL.LGIAQTVA.GGF.G...G......VT.
Retrocopy TPYMLIFGAFEIVFSQIPDFHEIWWLSIVAAVMSFTYSGVGLGLGIAQTVADGGFRGTIAGVT---NVTA

Parental  MQKVWRSLQAFGDIAFAYSYSIILIEIQDTIKAPPPSEAKVMKRATMVSVATTTVFYMLCGCMGYAAFGD
          .QK.WRSLQA.G.IAFA...S....EIQDTIKAPPPSEAKVMK.A...S...T.VFY.LCG.MGYAAFG.
Retrocopy TQKAWRSLQALGNIAFAFAFSNVYTEIQDTIKAPPPSEAKVMKQASLLSIVATSVFYALCGWMGYAAFGN

Parental  KSPDNLLTGFGFYEPFWLLDVANAAIVVHLVGAYQVFVQPIFAFVERWAAARWPDGGFISRELRVGPFSL
          ..PDNLLTGFGF.EPFWL.D.AN.AI.VHL.GAYQV..QP.FAFVER.A..RWPD.GF...ELRVGPF..
Retrocopy AAPDNLLTGFGFFEPFWLVDAANVAIAVHLIGAYQVYCQPVFAFVERKASRRWPDSGFVNSELRVGPFAI

Parental  SVFRLTWRTAFVCATTVVSMLLPFFGDVVGLLGAVSFWPLTVYFPVEMYIAQRGVRRGSARWLCLKVLSA
          S.FRL.WR..FVC.TTVV.M.LPFFG..VGLLGA.SFWPLTVY.P.EMYIAQRGVRRGSA.W..L..L..
Retrocopy SAFRLAWRSVFVCFTTVVAMALPFFGVIVGLLGAISFWPLTVYLPTEMYIAQRGVRRGSALWIGLRALAV

Parental  ACLVVSVAAAAGSIADVVDALKVYRPFSG
          A...VS.AA..G..A..V......RPFSG
Retrocopy AGFIVSAAATTGAVANFVGDFMKFRPFSG

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Oryza glaberrima was not studied using ChIP-Seq data.

EST

Oryza glaberrima was not studied using EST data.

TSS

Oryza glaberrima was not studied using FANTOM5 data.

Lab

retro_ogla_45 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza glaberrima 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryza glaberrima	ORGLA11G0052300	1 retrocopy	retro_ogla_45 ,