RetrogeneDB ID: retro_oind_44

Retrocopy location

• Organism: Rice subsp. indica (Oryza sativa indica)
• Coordinates: AAAA02042438.1:2124..3366(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BGIOSGA039379
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BGIOSGA003078
• Aliases: None
• Description: None

Sequence

>retro_oind_44
ATGCGTCCGGCGATCGCCGCTTCCGACAGCATCACCCGCACGGTGAACGAGATCCTCGACAACGTGAAGGCCAACGGCGA
TCGGGCGTTGCGCGACTACAGCGCCCGTTTCGACAAGGCGGAAGTCTCGACGCTGCGCGTCAGCGCCGAGCAGATCGCCG
CCGCCGCCGCGCGGTTGGGCGACGACATCAAACAGGCGATGGCGGTGGCCGTCGCCAACGTGGAAACCTTCCACAACGCG
CAGCGACTGCCGCCGGTGGACGTCGAAACGCAACCGGGCGTGCGCTGCCAGCAGGTGACCCGCCCAATCGACTCGGTGGG
CCTGTATATTCCCGGCGGATCGGCGCCGCTGTTCTCCACCGTGCTGATGCTGGCGACGCCGGCGCGCATCGCCGGCTGCC
GCCGGGTAGTGCTGTGCTCGCCGCCGCCGATCGCCGATGAGATCCTGTATGCGGCGCAGCTGTGCGGCGTGCAGGAAGTG
TTTCAGGTCGGGGGCGCGCAGGCGATCGCCGCCCTGGCGTTCGGCACCGAAAGCGTGCCGCGCGTAGCGAAGATCTTCGG
GCCGGGCAACGCCTTCGTGACCGAAGCCAAGCGGCAGGTCAGCCAGCGCCTTGACGGCGCGGCCATCGACATGCCGGCCG
GTCCTTCGGAAGTGCTGGTGATCGCCGACGCCGGCGCCACCCCGGCATTTGTCGCTTCCGATCTGCTGTCGCAGGCCGAG
CACGGCCCGGATTCGCAGGTGATCCTGCTGACGCCGGACGCGGCGATGGCGCAGGCGGTGGCCGAAGCGGTGGAAAGCCA
GCTGGCCGAGCTGCCGCGTGCTGAGACCGCCCGTCAGGCGCTGGCGAGCAGCCGCCTGATCGTGGCGCGCGATCTGCCGG
AGTGCGTGGCCATCAGCAACCGTTACGGCCCGGAGCACCTGATCATTCAGACCCGCAATGCGCGCGATCTGGTGGACGGC
ATCACCAGCGCCGGTTCGGTGTTCCTCGGCGACTGGTCGCCGGAGTCCGCCGGCGATTACGCCTCCGGCACCAACCACGT
GCTGCCGACCTACGGCTACACCGCTACCTGCTCAAGCCTTGGGCTGGCCGATTTCCAAAAACGCATGACGGTGCAGGAGC
TGACGCCGCAGGGCTTCAGCAACCTGGCCGCCACCATCGAGACGCTGGCTGCCGCCGAGCAGCTGATCGCCCACAAGAAC
GCCGTGACCCTGCGCGTCGCCGCCCTGAAGGAGCAAGCATGA

Alignment

ORF - retro_oind_44 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.24 %
• Parental protein coverage: 86.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RPRIDFS-SIFGTVNPIVEDVRMRGDAAVKDYTVKFDKVALDDVVVRVSDLPDV--ELDPAVKEAFDVAY
          RP.I..S.SI..TVN.I...V...GD.A..DY...FDK.......V...........L....K.A..VA.
Retrocopy RPAIAASDSITRTVNEILDNVKANGDRALRDYSARFDKAEVSTLRVSAEQIAAAAARLGDDIKQAMAVAV

Parental  DNIYAFHVSQKLPEKTVENMKGVRCKRITRCIGSVGLYVPGGTAVLPSTALMLAVPAQIAGCKTVVLATP
          .N...FH..Q.LP...VE...GVRC...TR.I.SVGLY.PGG.A.L.ST.LMLA.PA.IAGC..VVL..P
Retrocopy ANVETFHNAQRLPPVDVETQPGVRCQQVTRPIDSVGLYIPGGSAPLFSTVLMLATPARIAGCRRVVLCSP

Parental  PSRDGSICKEVLYCAKKAGVTHVLKAGGAQAISAMAWGTVSCPKVEKIFGPGNQYVTAAKMILQNSEAMV
          P.....I..E.LY.A...GV..V...GGAQAI.A.A.GT.S.P.V.KIFGPGN..VT.AK..........
Retrocopy PP----IADEILYAAQLCGVQEVFQVGGAQAIAALAFGTESVPRVAKIFGPGNAFVTEAKRQVSQRLDGA

Parental  SIDMPAGPSEVLVIADKYANPVHVAADLLSQAEHGPDSQVVLVVAGDGVDLGAIEAEVSKQCSALPRGEF
          .IDMPAGPSEVLVIAD..A.P..VA.DLLSQAEHGPDSQV.L....D.....A....V..Q...LPR.E.
Retrocopy AIDMPAGPSEVLVIADAGATPAFVASDLLSQAEHGPDSQVILLTP-DAAMAQAVAEAVESQLAELPRAET

Parental  ASKALGHSFTVFAKDMVEAISFSNMYAPEHLIINVKDAEQWEDLVENAGSVFLGQWTPESVGDYASGTNH
          A..AL..S....A.D..E....SN.Y.PEHLII....A....D....AGSVFLG.W.PES.GDYASGTNH
Retrocopy ARQALASSRLIVARDLPECVAISNRYGPEHLIIQTRNARDLVDGITSAGSVFLGDWSPESAGDYASGTNH

Parental  VLPTYGYARMYSGVSLNSFLKYITVQSLSEEGLRSLGPHVAKMAEVEGLEAHRRAVTLRL
          VLPTYGY....S...L..F.K..TVQ.L...G...L.......A..E.L.AH..AVTLR.
Retrocopy VLPTYGYTATCSSLGLADFQKRMTVQELTPQGFSNLAATIETLAAAEQLIAHKNAVTLRV

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_44 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	BGIOSGA003078	1 retrocopy	retro_oind_44 ,