RetrogeneDB ID: retro_oind_47

Retrocopy location

• Organism: Rice subsp. indica (Oryza sativa indica)
• Coordinates: 9:21096478..21097825(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BGIOSGA031260
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BGIOSGA008091
• Aliases: None
• Description: None

Sequence

>retro_oind_47
ATGGCGCTTCGACCACCGCGGCCGTGTCCGGCCGGCGTGCAGCAGCGGCAGCTCGACGTCGACAGCGCCGGCAACGCCAA
GACTTCCCCGGAACAGAAGCTCGAGTTGCTGGACCTGCAGGAGGAGGACGACGAGCTCATCTTCCTCGACGCCGACGACG
AGGAGGGACGCCAGCTGCGCGAGAAGCTGGAGTCGCTGGAGCGGGAGTTCTGCCTGCTGGATGAGCAGCGGGACAACGCG
CTGTTCCAGATTCACGTGCTGGAAGAGACGGTGCGCTTCCGCGAGGAGCTCGTCAGGTGGCTGACGGCGGTCACCCCCCT
CGTCGTCGCCCAGCTCGACGAGGTCGTCGACGAGCACCACGCCGTCGTGACGCTGGGCGACGGATGCGAGAGGAAGATGT
GCGTCGGCGTCGCCGGCTCGTTCGACCGCGGCCTCCTCAAGCCCTCGGCGAACGTCGCGCTGAACGGCCGGTCGCTCGCG
CTCGTCGGCGTGCTCCCCTCCGACGTCGCCGGCTGCTCGGCCGCGCGGTTCCTCGTGGCGGACGCCGACAAGCCGGGCGT
CGCCTACGGCGACATCGGCGGGTGCGAGGCGCAGAAGCGGGAGGTGCGCGAGGCCGTGGAGCTGCCGCTGACGCACCCGG
AGCTCTTCGCCGCCGCCGGCGTCGACCCGCCGCGCGGCGTGCTCCTGCACGGCCCGCCGGGCACCGGGAAGACCATGCTC
GCCAAGGCCGTCGCGCGCGAGACCTCGGCGGCGTTCTTCCGCGTGAACGCCGCCGAGCTCGCGCGGCACGACGGACCGAG
GGTGGTGCGCGACCTGTTCCGGCTCGCCAGGGACAGGGCGCCGGCCATCGTCTTCATCGACGAGGTGGACGCGATCGCGG
CGGCGCGGCAAGGCGGCGACGGCGACGACGGCGGCGCCAGGCGCCACGTGCAGCGCGTGCTGATTGAGCTGCTCACCCAG
ATGGACGGCTTCGACGAGTCCACCAACGTGCGGGTGATCATGGCGACGAACCGCGCCGACGACCTGGACCCGGCGCTGCT
CCGGCCGGGGCGGCTGGACCGCAAGGTGGAGTTCACCGCGCCCGAGAGCCCGGAGGAGAAGCGGCTGGTGCTGCAGACGT
GCACGGCGGGGATGAGCCTGGACGGCGACGTCGACCTCGACGCCCTGGCGGCGCGGCGCGACAAGCTCAGCGCCGCCGAG
ATCGCCGCCGTGTGCCGCGAGGCCGGCATGCAGGCCGTGCGCGACAGGCGGGGCGCGGTGACGGCGGACGACTTCGACAA
GGGATACCTCGCCGTCGTCGGCAAGAAGCCCGGCGACGTCGCCACCGAGTTCCACTTCTACAACTGA

Alignment

ORF - retro_oind_47 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.29 %
• Parental protein coverage: 76.92 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EDDDDLYGRLKSLQRHMEFVEIQEEYVKDEQKNLKRELLRAQEEVKRIQSV-PLVIGQFMEMVDGNNGIV
          E....L...L.SL.R.......Q..........L........E.V.....V.PLV..Q..E.VD.....V
Retrocopy EEGRQLREKLESLEREFCLLDEQRDNALFQIHVLEETVRFREELVRWLTAVTPLVVAQLDEVVDEHHAVV

Parental  --GSTTGSNYYVRILSTINRELLKPSASVALHRHSNALVDVLPPEA---DSSISLLGSSEKPNVTYTDIG
          ..G........V.......R.LLKPSA.VAL...S.ALV.VLP...........L.....KP.V.Y.DIG
Retrocopy TLGDGCERKMCVGVAGSFDRGLLKPSANVALNGRSLALVGVLPSDVAGCSAARFLVADADKPGVAYGDIG

Parental  GCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVAHHTTAAFIRVVGSEFVQK
          GC..QK.E.REAVELPLTH.EL....G.DPPRGVLL.GPPGTGKTMLAKAVA..T.AAF.RV...E....
Retrocopy GCEAQKREVREAVELPLTHPELFAAAGVDPPRGVLLHGPPGTGKTMLAKAVARETSAAFFRVNAAELARH

Parental  YLGEGPRMVRDVFRLAKENAPAIIFIDEVDAIATAR--FDAQTG-ADREVQRILMELLNQMDGFDQTVNV
          ....GPR.VRD.FRLA...APAI.FIDEVDAIA.AR...D...G.A.R.VQR.L.ELL.QMDGFD...NV
Retrocopy ---DGPRVVRDLFRLARDRAPAIVFIDEVDAIAAARQGGDGDDGGARRHVQRVLIELLTQMDGFDESTNV

Parental  KVIMATNRADTLDPALLRPGRLDRKIEFPLPDR-RQKRLVFQVCTAKMNLSDEVDLEDYVSRPDKISAAD
          .VIMATNRAD.LDPALLRPGRLDRK.EF..P.....KRLV.Q.CTA.M.L...VDL.....R.DK.SAA.
Retrocopy RVIMATNRADDLDPALLRPGRLDRKVEFTAPESPEEKRLVLQTCTAGMSLDGDVDLDALAARRDKLSAAE

Legend:

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

Expression

RNA-Seq

Oryza sativa indica was not studied using RNA-Seq expression data.

ChIP-Seq

Oryza sativa indica was not studied using ChIP-Seq data.

EST

Oryza sativa indica was not studied using EST data.

TSS

Oryza sativa indica was not studied using FANTOM5 data.

Lab

retro_oind_47 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza sativa indica 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 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA008091	1 retrocopy	retro_oind_47 ,
Aegilops tauschii	F775_28952	1 retrocopy	retro_atau_13,
Leersia perrieri	LPERR02G11870	1 retrocopy	retro_lper_5,
Oryza barthii	OBART02G14640	1 retrocopy	retro_obar_11,
Oryza punctata	OPUNC02G13140	1 retrocopy	retro_opun_13,
Oryza glaberrima	ORGLA02G0127200	1 retrocopy	retro_ogla_44,
Oryza sativa japonica	OS02G0325100	1 retrocopy	retro_osat_48,
Triticum aestivum	Traes_2AL_80D15B4FB	2 retrocopies	retro_taes_103, retro_taes_107,