RetrogeneDB ID: retro_oind_61

Retrocopy location

• Organism: Rice subsp. indica (Oryza sativa indica)
• Coordinates: AAAA02041077.1:3059..4598(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BGIOSGA039107
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BGIOSGA008337
• Aliases: None
• Description: None

Sequence

>retro_oind_61
ATGGTGCCGGAAGCGGCGGTCGCGATGCTGGCCTGCGCCCGCATCGGCGCCGTACATTCGGTGATCTTCGGCGGCTTCTC
GCCGGAAGCGGTCGCCGGACGCATTATCGACTCCAACGCCAAACTGGTGATCACCGCCGATGAAGGCCTGCGCGCCGGCC
GCGCCGTGCCGCTGAAAAAGAACGTCGACGATGCGCTGAAAAACCCCGGCGTGGTCAGCGTGGCCAACGTCGTGGTGTTC
CAGCGCACCGGCAAACCGGGTTACTGGCAGGAAGGGCGCGATCTGTGGTGGCATGAGCTGACCCAGGGCGTTTCCGCCGA
TTGCCCGCCGGAAGAAGTGAACGCCGAAGATCCGCTGTTTATCCTGTACACCTCCGGCTCGACCGGCAAGCCAAAAGGCG
TGCTGCACACCACCGGCGGCTACCTGGTGTACGCCGCGATGACCTTTAAGTATGTGTTCGACTATCACGACGGCGACATT
TACTGGTGCACCGCCGACGTGGGCTGGGTCACCGGTCACAGCTATCTGCTGTACGGCCCGCTGGCCTGCGGCGCCACCAC
GCTGATGTTCGAAGGCGTACCTAACTATCCGGGCGTCAATCGTCTGTCGCAGGTGATAGACAAACACCAGGTCAACATTC
TGTATACCGCGCCGACCGCCATTCGTGCCCTGATGGCCGAAGGCGACAAGGCGATCGAAGGCACCCGACGCGATTCGCTG
CGCATCATGGGCTCGGTCGGCGAACCGATCAACCCGGAAGCCTGGGAGTGGTACTACAACAAGATAGGCAACGCCAAATG
CCCGATCGTCGACACCTGGTGGCAAACCGAAACCGGCGGCTTCATGATTACCCCGCTGCCGGGCGCCACCGAGCTGAAGG
CCGGTTCCGCCACGCGGCCTTTCTTCGGCGTACAGCCGGCGCTGGTCGATAATGTCGGCACGCCGCAGGAAGGCGCCTGC
GAAGGCAACCTGGTGATCGTCGATTCCTGGCCGGGCCAGGCGCGCACCCTGTTCGGCGATCATGACCGCTTCGAGCAAAC
CTACTTCTCGACCTTCAAAGGCATGTATTTCAGCGGCGACGGCGCCCGCCGCGACGAGGACGGTTACTACTGGATCACCG
GCCGCGTCGATGACGTGCTGAACGTCTCCGGCCACCGTTTGGGCACCGCCGAGATCGAGTCCGCGCTGGTATCTCACCCG
AAAATCGCCGAAGCGGCGGTGGTCGGCATTCCTCATAACATCAAAGGCCAGGCGATCTACGCCTATATCACGCTGAACCA
CGGCGAAGAACCGACGCCGGAGCTCTATGCCGAAGTGCGCAACTGGGTGCGCAAAGAGATAGGGCCGATCGCCACGCCGG
ACGTGCTGCACTGGACAGACTCGCTGCCCAAAACGCGCTCCGGCAAGATCATGCGGCGTATCCTGCGCAAAATTGCCGCC
GGCGACACCAGCAACCTGGGGGATACCTCCACGCTGGCGGATCCGGCTGTAGTCGACAAGCTGTTGGAAGAAAAACAATC
AATGAAAGTGCCGTCATAA

Alignment

ORF - retro_oind_61 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.03 %
• Parental protein coverage: 59.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  WQAGRDVWWQDVVTSFPTKCDVEWVDAEDPLFLLYTSGSTGKPKGVLHTTGGYMVYSATTFKYAFDYKPS
          WQ.GRD.WW..........C..E.V.AEDPLF.LYTSGSTGKPKGVLHTTGGY.VY.A.TFKY.FDY...
Retrocopy WQEGRDLWWHELTQGVSADCPPEEVNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAAMTFKYVFDYHDG

Parental  DIYWCTADCGWITGHSYVTYGPLLNGATVLVFEGTPNYPDSGRCWDIVDKYKVTIFYTAPTLVRSLMRDG
          DIYWCTAD.GW.TGHSY..YGPL..GAT.L.FEG.PNYP...R.....DK..V.I.YTAPT..R.LM..G
Retrocopy DIYWCTADVGWVTGHSYLLYGPLACGATTLMFEGVPNYPGVNRLSQVIDKHQVNILYTAPTAIRALMAEG

Parental  TEYVTRHSRKSLRVLGSVGEPINPSAWRWFYNIVGDSRCPISDTWWQTETGGFMITPLPGAWPQKPGSAT
          ........R.SLR..GSVGEPINP.AW.W.YN..G...CPI.DTWWQTETGGFMITPLPGA...K.GSAT
Retrocopy DKAIEGTRRDSLRIMGSVGEPINPEAWEWYYNKIGNAKCPIVDTWWQTETGGFMITPLPGATELKAGSAT

Parental  FPFFGVQPVIVDEKGKEIEGECSGYLCIKKSWPGAFRTLYGDHDRYETTYFKPFAGYYFTGDGCSRDKDG
          .PFFGVQP..VD..G...EG.C.G.L.I..SWPG..RTL.GDHDR.E.TYF..F.G.YF.GDG..RD.DG
Retrocopy RPFFGVQPALVDNVGTPQEGACEGNLVIVDSWPGQARTLFGDHDRFEQTYFSTFKGMYFSGDGARRDEDG

Parental  YHWLTGRVDDVINVSGHRIGTAEVESALVSHPKCAEAAVVAVEHEVKGQGIYAFVTLVDGVPYSEELRKS
          Y.W.TGRVDDV.NVSGHR.GTAE.ESALVSHPK.AEAAVV...H..KGQ.IYA..TL..G.....EL...
Retrocopy YYWITGRVDDVLNVSGHRLGTAEIESALVSHPKIAEAAVVGIPHNIKGQAIYAYITLNHGEEPTPELYAE

Parental  LILTVRNQIGAFAAPDKIHWAPGLPKTRSGKIMRRILRKIASKQLDELGDTSTLADPGVVDQLIALK
          ....VR..IG..A.PD..HW...LPKTRSGKIMRRILRKIA......LGDTSTLADP.VVD.L...K
Retrocopy VRNWVRKEIGPIATPDVLHWTDSLPKTRSGKIMRRILRKIAAGDTSNLGDTSTLADPAVVDKLLEEK

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_61 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA008337	1 retrocopy	retro_oind_61 ,