RetrogeneDB ID: retro_oglu_3

Retrocopy location

• Organism: Oryza glumaepatula
• Coordinates: 12:5544362..5545769(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OGLUM12G06330
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OGLUM12G05640
• Aliases: None
• Description: None

Sequence

>retro_oglu_3
ATGGTTCAGATCGAGCCGCTCGAGGTGTCGCTGGAGGCCGGCAACCAGGCGGACTCGGCGTTGCTCGACGACGACGGGCG
GCCGCGCCGCACCGGCACGTTCTGGACGGCGAGCGCGCACATCATCACCGCCGTGATCGGGTCCGGGGTGCTGTCGCTGC
CGTGGGCGACGGCGCAGCTCGGGTGGGTCGCCGGGCCCGCCGTGATGGTGGTGTTCGGCGGCGTCACCTACTTCACCGCC
ACGCTCCAGGCCGAGTGCTACCGCACCGGCGACGAGGAGACCGGCGCCCGCAACTACACCTACATCGGCGCCGTGCGCGC
CATCCTCGGCGGCCCCAACGCCAAGCTCTGCGGCATCATCCAGTACGCCAACCTCGTCGGCACCGCCATCGGCTACACCA
TCGCCGCCTCCATCAGCATGCAGGCCATCAAGAGGGCGGGCTGCTTCCACGCCAATGGCCACAACGTCCCGTGCCGCATC
TCGAGCACCCCGTACATGCTCATCTTCGGCGCCTTCGAGATCGTCTTCTCGCAGATCCCCGACTTCCACGAGATCTGGTG
GCTGTCCATCGTCGCCGCCGTCATGTCCTTCACCTACTCCGGCGTCGGCCTCGGCCTCGGCATCGCCCAGACCGTCTCCG
ACGGCGGGTTCCGCGGCACGATCGCCGGCGTCACCAACGTCACCGCCACGCAGAAGGCGTGGCGGTCGCTGCAGGCGCTG
GGCAACATCGCCTTCGCGTTCGCCTTCTCCAACGTGTACACCGAGATCCAGGACACGATCAAGGCGCCGCCGCCGTCAGA
GGCGAAGGTGATGAAGCAGGCATCGCTGCTGAGCATCGTGGCGACGTCGGTGTTCTACGCGCTGTGCGGGTGGATGGGTT
ACGCGGCGTTCGGCAACGCGGCGCCGGACAACCTCCTCACCGGATTCGGCTTCTTCGAGCCGTTCTGGCTCGTCGACGCC
GCCAACGTCGCCATCGCCGTGCACCTCATCGGCGCCTACCAGGTGTACTGCCAGCCGGTCTTCGCCTTCGTCGAGCGCAA
GGCGTCGCGCCGGTGGCCCGACAGCGGCTTCGTCAACAGCGAGCTCCGGGTGGGGCCCTTCGCCATCAGCGCGTTCCGGC
TGGCGTGGCGCTCGGTGTTCGTCTGCTTCACCACCGTGGTCGCCATGGCGCTGCCCTTCTTCGGCGTCATCGTCGGCCTC
CTCGGTGCCATCTCCTTCTGGCCGCTCACCGTCTACCTCCCCACGGAGATGTACATCGCGCAGCGCGGCGTGCGGCGCGG
CAGCGCACTGTGGATCGGGCTCAGGGCGCTCGCCGTCGCCGGCTTCGTCGTGTCGGCCGCCGCCACCACGGGCGCCGTCG
CCAACTTCGTCGGCGACTTCATGAAATTCCGTCCCTTCAGTGGATAG

Alignment

ORF - retro_oglu_3 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.58 %
• Parental protein coverage: 98.53 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VKPMEVSVEAGNAGEAAWLDDDGRARRTGTFWTASAHIITAVIGSGVLSLAWAIAQLGWVAGPAVMLLFA
          ..P.EVS.EAGN....A.LDDDGR.RRTGTFWTASAHIITAVIGSGVLSL.WA.AQLGWVAGPAVM..F.
Retrocopy IEPLEVSLEAGNQADSALLDDDGRPRRTGTFWTASAHIITAVIGSGVLSLPWATAQLGWVAGPAVMVVFG

Parental  FVIYYTSTLLAECYRTGDPTTGKRNYTYMDAVRANLGGAKVTFCGVIQYANLVGVAIGYTIASSISMRAI
          .V.Y.T.TL.AECYRTGD..TG.RNYTY..AVRA.LGG.....CG.IQYANLVG.AIGYTIA.SISM.AI
Retrocopy GVTYFTATLQAECYRTGDEETGARNYTYIGAVRAILGGPNAKLCGIIQYANLVGTAIGYTIAASISMQAI

Parental  RRAGCFHHNGHGDPCRSSSNPYMILFGVVQIVFSQIPDFDQIWWLSIVAAVMSFTYSGIGLSLGIVQTIS
          .RAGCFH.NGH..PCR.SS.PYM..FG...IVFSQIPDF..IWWLSIVAAVMSFTYSG.GL.LGI.QT.S
Retrocopy KRAGCFHANGHNVPCRISSTPYMLIFGAFEIVFSQIPDFHEIWWLSIVAAVMSFTYSGVGLGLGIAQTVS

Parental  NGGIQGSLTGISIGVGVSSTQKVWRSLQAFGDIAFAYSFSNILIEIQDTIKAPPPSEAKVMKSATKLSVA
          .GG..G...G......V..TQK.WRSLQA.G.IAFA..FSN...EIQDTIKAPPPSEAKVMK.A..LS..
Retrocopy DGGFRGTIAGVT---NVTATQKAWRSLQALGNIAFAFAFSNVYTEIQDTIKAPPPSEAKVMKQASLLSIV

Parental  TTTVFYMLCGCMGYAAFGDAAPDNLLTGFGFYEPFWLLDVANVAIVVHLVGAYQVFVQPIFAFVERWASR
          .T.VFY.LCG.MGYAAFG.AAPDNLLTGFGF.EPFWL.D.ANVAI.VHL.GAYQV..QP.FAFVER.ASR
Retrocopy ATSVFYALCGWMGYAAFGNAAPDNLLTGFGFFEPFWLVDAANVAIAVHLIGAYQVYCQPVFAFVERKASR

Parental  RWPDSAFITKELRVGPFALSLFRLTWRSAFVCLTTVVAMLLPFFGNVVGLLGAVSFWPLTVYFPVEMYIA
          RWPDS.F...ELRVGPFA.S.FRL.WRS.FVC.TTVVAM.LPFFG..VGLLGA.SFWPLTVY.P.EMYIA
Retrocopy RWPDSGFVNSELRVGPFAISAFRLAWRSVFVCFTTVVAMALPFFGVIVGLLGAISFWPLTVYLPTEMYIA

Parental  QRGVPRGSARWVSLKTLSACCLVVSIAAAAGSIADVIDALKVYRPFSG
          QRGV.RGSA.W..L..L.....VVS.AA..G..A.........RPFSG
Retrocopy QRGVRRGSALWIGLRALAVAGFVVSAAATTGAVANFVGDFMKFRPFSG

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Oryza glumaepatula was not studied using ChIP-Seq data.

EST

Oryza glumaepatula was not studied using EST data.

TSS

Oryza glumaepatula was not studied using FANTOM5 data.

Lab

retro_oglu_3 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza glumaepatula 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza brachyantha	OB12G14670	1 retrocopy	retro_obra_17,
Oryza glumaepatula	OGLUM12G05640	1 retrocopy	retro_oglu_3 ,
Oryza punctata	OPUNC12G04770	1 retrocopy	retro_opun_43,
Triticum aestivum	Traes_5DL_BB10A3B4B	2 retrocopies	retro_taes_215, retro_taes_217,