RetrogeneDB ID: retro_oind_38

Retrocopy location

• Organism: Rice subsp. indica (Oryza sativa indica)
• Coordinates: 7:13692598..13694095(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BGIOSGA025614
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BGIOSGA017675
• Aliases: None
• Description: None

Sequence

>retro_oind_38
ATGGCGGCGGCGGCGGTGGCGGCAGATCAGAAGGTGGTGACGATGACGAGCCTCCGGGAGGGCTGCGCTTGCGCGGCGCC
TCCTGATGCAGCTGCGCCGCCGATGCCGAAGATGGCGGCGGCGCAGAGGGTGGTGGCGGAGCTGAGAGAGGCGTGCGCGA
TGCCGGCGGCGAGGCTGGCGGAGGTGGCCGCGGCGATGGCCGGCGAGATGGAGGCCGGGCTGGCGGTGGAGGGCGGCAGC
AGCGAGATGAAGATGATCGTGTCGTACGTCGACAGCCTCCCCACCGGCGGCGAGGAGGGGTCGTTCTACGCGCTCGACCT
CGGCGGCACCAACTTCCGCGTCCTCCGCGTGCGGCTTGCCGGCGGCGGCGTCGCCGAGCGCGTGGCGAGGGAGGTCCCGA
TCCCTCCCGGCCTCATGTCCGGCGGCGGCGCCACCTCGGAGTGCCTCTTCGGCTTCATCGCCTCCGCGCTAGCCGAGTTC
GTCGGCGAGGAGGAAGAAGAAGGCGGCCTCGACGGCGGCGAGAGGGAGCTTGGGTTCACCTTCTCCTTCCCCGTGCACCA
AACCTCCATCGCGTCGGGGACGCTCATCCGGTGGACGAAGGCGTTCGCCGTCGACGACGCGATCGGCGAGGACGTCGTGG
CGGCGCTGCAGGCGGCCATGTCGGAGCGGGGGCTCGACATGCGCGTGTCGGCGCTCATCAACGACACCGTCGGGACGCTC
GCCGCGGGCAGCTACTACGACGAGGACGTCGTGGCCGCCGTCATCCTCGGCACCGGCACGAACGCCTCCTACGTCGAGGA
CGCCACCGCCATCGCCAAGCTACACCCATCGCAGCTGCCAGCATCGAACACCATGGTGATCAACACCGAGTGGGGCAGCT
TCGCCTCGCCGTGCCTCCCATTGACGGAGTTCGACGAAGCACTCGATCAGGAGAGCCTCAACCCCGGCGAGCAGACCTAC
GAGAAGCTCATCTCCGGGATGTACCTCGGCGAGATCGTCAGGAGGGTCCTCCTCAAGATCTCCTCCCGGTGCCCCTCCCT
CCTCGGCGGCGCCGGCGAGCTCGCGACGCCGTTCGTCCTCAGGACACCCGACGTGTCCGCGATGCACCACGACGAGACGC
CCGACCTGAGCATCGTCGGCGAGAAGCTGGAACGCACGCTGGGAATCCGCGGCACGTCGCCGGAGGCGAGGAGGATGGTC
GTCGAGGTGTGCGACATCGTCGCCACGAGGGCCGCCCGGCTGGCCGCGGCGGGGATCGTCGGGATCCTGAAGAAGATCGG
GAGGGTCGACGGCGGCGAGGGGCGGAGGAGGAGGTCGGTGGTCGCCGTGGACGGCGGGCTGTTCGAGCACTACGGCAAGT
TCCGGCGGTGCATGGAGAGCGCGGTGAGGGAGCTGCTCGGAGAGGCGGCGGCGGAGAGGGTGGTCGTCAAGCTCGCCAGC
GACGGCTCCGGGCTCGGCGCCGCCCTGGTTGCAGCTGCTCACTCGCAGAGAGCATAA

Alignment

ORF - retro_oind_38 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.91 %
• Parental protein coverage: 91.9 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ADAVLRELEERCAAPPARLRQVADAMAVEMHAGLASEGGS-KLKMIISYVDALPSGEEKGVFYALDLGGT
          A..V..EL.E.CA.P.ARL..VA.AMA.EM.AGLA.EGGS...KMI.SYVD.LP.G.E.G.FYALDLGGT
Retrocopy AQRVVAELREACAMPAARLAEVAAAMAGEMEAGLAVEGGSSEMKMIVSYVDSLPTGGEEGSFYALDLGGT

Parental  NFRVLRVQLGGKEGRVIKQEHDEISIPPHLMTGG---SNELFDFIASSLAKFVASEGEDFHLAEGRQREL
          NFRVLRV.L.G..G.V......E..IPP.LM.GG...S..LF.FIAS.LA.FV..E.E...L..G..REL
Retrocopy NFRVLRVRLAG--GGVAERVAREVPIPPGLMSGGGATSECLFGFIASALAEFVGEEEEEGGL-DGGEREL

Parental  GFTFSFPVKQTSIASGTLINWTKGFSIDETVGEDVVTELTKALERQGLDMKVTALINDTIGTLAGGRYDD
          GFTFSFPV.QTSIASGTLI.WTK.F..D...GEDVV..L..A....GLDM.V.ALINDT.GTLA.G.Y.D
Retrocopy GFTFSFPVHQTSIASGTLIRWTKAFAVDDAIGEDVVAALQAAMSERGLDMRVSALINDTVGTLAAGSYYD

Parental  NDVIAAVILGTGTNAAYVERANAIPKWH-DLLPKSGDMVINMEWGNFRSSHLPLTEFDQALDAESLNPGE
          .DV.AAVILGTGTNA.YVE.A.AI.K.H...LP.S..MVIN.EWG.F.S..LPLTEFD.ALD.ESLNPGE
Retrocopy EDVVAAVILGTGTNASYVEDATAIAKLHPSQLPASNTMVINTEWGSFASPCLPLTEFDEALDQESLNPGE

Parental  QVYEKLISGMYLGEIVRRVLLKMAEEA-SLFGDEVPPKLKIPFIIRTPYMSMMHCDRSPDLRTVGAKLKD
          Q.YEKLISGMYLGEIVRRVLLK......SL.G......L..PF..RTP..S.MH.D..PDL..VG.KL..
Retrocopy QTYEKLISGMYLGEIVRRVLLKISSRCPSLLGG--AGELATPFVLRTPDVSAMHHDETPDLSIVGEKLER

Parental  ILGVQSTSLKTRRLVVDVCDIVAKRAACLAAAGIHGILKKLGR-DVPNTDKQRTVIAVNGGLYEHYTIFA
          .LG...TS...RR.VV.VCDIVA.RAA.LAAAGI.GILKK.GR.D.......R.V.AV.GGL.EHY..F.
Retrocopy TLGIRGTSPEARRMVVEVCDIVATRAARLAAAGIVGILKKIGRVDGGEGRRRRSVVAVDGGLFEHYGKFR

Parental  ECVESTLRDVLGEEVSSTIVIKLAKDGSGIGAALLAAAHSQ
          .C.ES..R..LGE......V.KLA.DGSG.GAAL.AAAHSQ
Retrocopy RCMESAVRELLGEAAAERVVVKLASDGSGLGAALVAAAHSQ

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_38 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA017675	1 retrocopy	retro_oind_38 ,
Oryza barthii	OBART05G23750	1 retrocopy	retro_obar_3,
Oryza glumaepatula	OGLUM05G25120	1 retrocopy	retro_oglu_6,
Oryza nivara	ONIVA05G24490	1 retrocopy	retro_oniv_15,
Oryza rufipogon	ORUFI05G25500	1 retrocopy	retro_oruf_35,