RetrogeneDB ID: retro_opun_43

Retrocopy location

• Organism: Red rice (Oryza punctata)
• Coordinates: 12:5059946..5061353(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OPUNC12G05320
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OPUNC12G04770
• Aliases: None
• Description: None

Sequence

>retro_opun_43
ATGGTTCAGATCGAGCCGCTCGAGGTGTCCCTGGAGGCCGGCAACCAGGCGGACTCGGCGTTGCTCGACGACGACGGCCG
GCCGCGCCGCACCGGCACGGTCTGCACGGCGAGTGCGCACATCATCACCGCCGTGATCGGCTCCGGGGTGCTGTCGCTGC
CGTGGGCGACGGCGCAGCTCGGGTGGATCGCCGGACCCGCCGTGATGGTGGTGTTCGGCGGCGTCACCTACTACACCGCC
ACGCTCCAGGCCGAGTGCTACCGCACCGGCGACGAGGAGACCGGGGGCCGTAATTACACCTACATCGGCGCCGTCCGCTC
CATCCTCGGCGGCGCCAATGTCAAGCTCTGCGGCATCATCCAGTACGCCAACCTCGTCGGCACCGCCATCGGCTACACCA
TCGCCGCCTCCATCAGCATGCAGGCCATCAAGAGGGCAGGCTGCTTCCACGCCAATGGCCACAACGTCCCGTGCCACAGC
TCGAGCACCCCGTACATGTTAATCTTCGGCGCCTTCGAGATCGTCTTCTCGCAGATCCCCGACTTCCACGAGATCTGGTG
GCTGTCCATCGTCGCCGCCGTCATGTCCTTCACCTACTCCGGCGTCGGCCTCGGCCTCGGCATCGCCCAGACCGTCGCCG
ACGGCGGGTTCCGTGGCACGATCGCCGGCGTAACCAACGTCACCACCATGCAGAAGGTGTGGCAGTCGCTGCAGGCGCTG
GGCAACATCGCCTTCGCGTTCTCCTTCTCCAATGTGTTCACCGAGATCCAGGACACGATCAAGGCGCCGCCGCCGTCGGA
GGCGAAGGTGATGAAGAAGGCGTCGGCGATGAGCATCTTGGCGACGTCGGTGTTCTACGCGCTGTGCGGGTGGATGGGCT
ACGCGGCGTTCGGCAACGCCGCGCCGGACAACCTCCTCACAGGATTCGGATTCTTCGAGCCCTTCTGGCTCGTCGACGCC
GCCAACGTCGCCATCGCCGTGCACCTCATCGGCGCCTACCAGGTGTTCTGCCAGCCAGTCTTCGCCTTGGTCGAGCGCAA
GGCGTCGCTCCGGTGGCCCGACAGCGGCTTCATCAACAGCGAGCTCCGCGTGGGTCCATTCGCCATCAGCACGTTCCGGC
TGTTATGGCGTTCGGCGTTCGTGTGCCTCACCACCGTGGTCGCCATGGCGCTGCCATTCTTCGGCGTCATCGTCGGCCTC
CTCGGCGCCATCTCCTTCTGGCCGCTCACCGTCTACCTCCCCACGGAGATGTACATCGCGCAGCGCGGCGTGCAACGCGG
CAGCGCACGGTGGATCGGACTCAGGGCGCTCGCCGTCGCCGGTTTCGTCGTGTCGGCCGCCGCCACCACCGGAGCCGTCG
CCAACTTCGTCAGCGAGTTCAACAAATTCCGTCCCTTCAGTGGATAG

Alignment

ORF - retro_opun_43 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.79 %
• Parental protein coverage: 97.91 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VKPMEVSVEAGNAGEAAWLDDDGRPRRTGTFWTASAHIITAVIGSGVLSLAWAIAQLGWVAGPAVMLLFA
          ..P.EVS.EAGN....A.LDDDGRPRRTGT..TASAHIITAVIGSGVLSL.WA.AQLGW.AGPAVM..F.
Retrocopy IEPLEVSLEAGNQADSALLDDDGRPRRTGTVCTASAHIITAVIGSGVLSLPWATAQLGWIAGPAVMVVFG

Parental  FVIYYTSTLLAECYRTGDPTTGKRNYTYMDAVRANLGGAKVTFCGVIQYANLVGVAIGYTIASSISMRAI
          .V.YYT.TL.AECYRTGD..TG.RNYTY..AVR..LGGA.V..CG.IQYANLVG.AIGYTIA.SISM.AI
Retrocopy GVTYYTATLQAECYRTGDEETGGRNYTYIGAVRSILGGANVKLCGIIQYANLVGTAIGYTIAASISMQAI

Parental  RRAGCFHHNGHGDPCRSSSNPYMILFGVVQIVFSQIPDFDQIWWLSIVAAVMSFTYSGIGLSLGIVQTIS
          .RAGCFH.NGH..PC.SSS.PYM..FG...IVFSQIPDF..IWWLSIVAAVMSFTYSG.GL.LGI.QT..
Retrocopy KRAGCFHANGHNVPCHSSSTPYMLIFGAFEIVFSQIPDFHEIWWLSIVAAVMSFTYSGVGLGLGIAQTVA

Parental  NGGIQGSLTGISIGVGVSSTQKVWRSLQAFGDIAFAYSFSNILIEIQDTIKAPPPSEAKVMKNATRLSVA
          .GG..G...G......V...QKVW.SLQA.G.IAFA.SFSN...EIQDTIKAPPPSEAKVMK.A...S..
Retrocopy DGGFRGTIAGVT---NVTTMQKVWQSLQALGNIAFAFSFSNVFTEIQDTIKAPPPSEAKVMKKASAMSIL

Parental  TTTVFYMLCGCMGYAAFGDAAPDNLLTGFGFYEPFWLLDVANVAIVVHLVGAYQVFVQPIFAFVERWASR
          .T.VFY.LCG.MGYAAFG.AAPDNLLTGFGF.EPFWL.D.ANVAI.VHL.GAYQVF.QP.FA.VER.AS.
Retrocopy ATSVFYALCGWMGYAAFGNAAPDNLLTGFGFFEPFWLVDAANVAIAVHLIGAYQVFCQPVFALVERKASL

Parental  RWPDSAFIAKELSVGPFALSLFRLTWRSAFVCLTTVVAMLLPFFGNVVGLLGAVSFWPLTVYFPVEMYIA
          RWPDS.FI..EL.VGPFA.S.FRL.WRSAFVCLTTVVAM.LPFFG..VGLLGA.SFWPLTVY.P.EMYIA
Retrocopy RWPDSGFINSELRVGPFAISTFRLLWRSAFVCLTTVVAMALPFFGVIVGLLGAISFWPLTVYLPTEMYIA

Parental  QRGVPRGSARWISLKTLSACCLVVSIAAAAGSIADVIDALKVYRPFSG
          QRGV.RGSARWI.L..L.....VVS.AA..G..A.........RPFSG
Retrocopy QRGVQRGSARWIGLRALAVAGFVVSAAATTGAVANFVSEFNKFRPFSG

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Oryza punctata was not studied using ChIP-Seq data.

EST

Oryza punctata was not studied using EST data.

TSS

Oryza punctata was not studied using FANTOM5 data.

Lab

retro_opun_43 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza punctata 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA037101	1 retrocopy	retro_oind_7,
Oryza brachyantha	OB12G14670	1 retrocopy	retro_obra_17,
Oryza glumaepatula	OGLUM12G05640	1 retrocopy	retro_oglu_3,
Oryza nivara	ONIVA12G04480	1 retrocopy	retro_oniv_32,
Oryza punctata	OPUNC12G04770	1 retrocopy	retro_opun_43 ,
Triticum aestivum	Traes_5DL_BB10A3B4B	2 retrocopies	retro_taes_215, retro_taes_217,