RetrogeneDB ID: retro_oind_62

Retrocopy location

• Organism: Rice subsp. indica (Oryza sativa indica)
• Coordinates: 8:23533574..23535692(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BGIOSGA028775
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BGIOSGA006938
• Aliases: None
• Description: None

Sequence

>retro_oind_62
ATGTCGCCGGCTGCGGCGGCGGCGCTGGCGGAGGCTCCCGGGGTGGCGGCGGTGGTGCCGGAGCGGGTCCGGCAGCTCGC
CACCACCCGCTCGCCGCGGTTCCTTGGGCTGCTGTCGTCCCCGCCGTCGGCGCTCCTCGCGGACTCGGATTTTGGTTCCG
ACCTCGTCATCGCCATCATCGACACCGGCATCTCCCCCACCCACCGCAGCTTCCACGACCGTGGGCTTGGTCCGGTGCCG
TCCAAGTGGCGCGGGGTGTGCTCGTCGGGGCCTGGGTTCCCGCCCAACTCCTGCAATCGCAAGCTCGTCGGCGCGCGGTT
CTTCTCCGCCGGGTATGAGGCCACCTCTGGCCGCATGAACGAGACGGCGGAGGTCAGGTCGCCGCTCGACACCGATGGGC
ACGGGACCCACACGGCCTCCATCGCCGCCGGCCGCTACGTGTTCCCGGCGTCCACCCTCGGCTACGCCCGGGGCGTGGCT
GCCGGGATGGCGCCCAAGGCACGCCTCGCCGCGTACAAGGTGTGCTGGGTGGGCGGCTGCTTCGACTCCGACATCCTTGC
GGCTTTCGATGCCGCCGTCGCCGACGGCGTCGATGTCGTGTCCCTCAGCGTCGGTGGCGTCGTCGTGCCGTACTACCTTG
ACGCCATTGCCATTGGGGCATTCGGGGCGACGGAGGCTGGGATTGTTGTTTCGGCTTCGGCCGGCAATGGCGGCCCTGGT
GGGCTCACTGTGACCAATGTGGCTCCCTGGATGGCCACCGTTGGCGCTGGGTCCATGGACCGCGCCTTCCCGGCCAACGT
GCAGCTCGGCAATGGTCAAGTGCTCGACGGTGTTAGCGTGTACGGCGGGCCAGCGCTCCAATCCGGCAAGATGTATGAGC
TTGTATATGCTGGAGCAAGCAGCGGCGCTGCCTCGTCTGCGGCTGACGGCTACTCGGCGTCCATGTGCCTCGACGGCTCG
CTCGACCCCGCCGCGGTGCGGGGCAAGATCGTGGTGTGCGACCGCGGCGTGAACTCGCGCGCCGCCAAGGGCGACGTGGT
TCACCGCGCGGGCGGCATCGGGATGGTGCTCGCCAACGGGGTGTTCGACGGGGAGGGCCTCGTCGCCGACTGCCACGTTC
TGCCAGCCACAGCCGTCGGTGCGGCCGCTGGCGACAAGCTCCGTAAGTACATTGGGTCGTCGACGCGGCAGGCGCCGGCC
ACCGGCACCATCTTGTTCGAAGGCACCCACCTCGGCGTGCATCCGGCGCCTGTGGTGGCCGCGTTCTCCGCGCGTGGCCC
CAATCCCCAATCCCCGGAGATACTCAAGCCAGACCTGATTGCCCCCGGCCTAAACATCCTCGCCGCATGGCCCAGCGGCG
TCGGGCCGGCCGGCATCCCCTCCGACGGCCGCCGCACGGAATTCAACATCCTCTCGGGCACGTCCATGGCTTGCCCGCAC
ATCTCCGGCCTCGCCGCATTGCTCAAGGCGGCGCATCCTACCTGGAGCCCCGCGGCGATCAAGTCAGCGCTCATGACCAC
CGCCTACATCAAGGACAACAGCAACGGCACCATGGTGGACGAGTCCACGGGCGTCGTGGCCGACGTGTTCGACTTCGGCG
CAGGGCACGTTGACCCGATGCGCGCCATGGACCCTGGTCTCGTCTACGACATCACCCCCGTGGACTACGTCAACTTCCTC
TGCAACCTGAACTACACCGAGCAGAACATCCGGGCGATCACGCGGCGCCCCGCGGACTGCCGCGGCGCGCGGCGCGCGGG
GCACGCCGGGAACCTCAACTACCCGTCCATGTCCGCCACGTTCGCCGCGGACGGCACCAGGGCGACGATGAAGACCCACT
TCATCCGGACGGTGACCAACGTCGGCGGCGGGCGCGCGGTGTACCGCGCGACGGTGAGGTCGCCCGAGGGGTGCGCGGTG
ACCGTGCAGCCGCGGCAGCTGGCGTTCCGGCGCGACGGGCAGAAGCTGAGCTTCACGGTGCGGGTGGAGGCCGCGGCGCC
GGCCAAGAAGATGGAGCCCGGGAGCTCGCAGGTGAGGAGCGGCGCGGTGACGTGGAGCGACGGGAGGCACGCCGTGAACA
CCCCGGTCGTCGTGACAGTGCAAGCGCCGCTGCAGTAA

Alignment

ORF - retro_oind_62 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.17 %
• Parental protein coverage: 71.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LDAAAAAKIAEKPGVVSVFPNRGHKLHTTRSWQFLGLAGVGGAPTGAAWKKARFGEDTIIGNLDTGVWPE
          ...AAAA..AE.PGV..V.P.R...L.TTRS..FLGL......P..A......FG.D..I...DTG..P.
Retrocopy MSPAAAAALAEAPGVAAVVPERVRQLATTRSPRFLGLLS---SPPSALLADSDFGSDLVIAIIDTGISPT

Parental  SESFRDDGLGPIPSWWRGECQKGQD-DAFSCNRKLIGARFFNKGYASAVGNLN-TSLFDTPRDTDGHGTH
          ..SF.D.GLGP.PS.WRG.C..G......SCNRKL.GARFF..GY....G..N.T.....P.DTDGHGTH
Retrocopy HRSFHDRGLGPVPSKWRGVCSSGPGFPPNSCNRKLVGARFFSAGYEATSGRMNETAEVRSPLDTDGHGTH

Parental  TLSTAGGAPVAGASVFGYGNGTASGGSPMARVAAYRVCYTPVNGSECFDADILAAFDAAIHDGVHVLSVS
          T.S.A.G..V..AS..GY..G.A.G..P.AR.AAY.VC...V.G..CFD.DILAAFDAA..DGV.V.S.S
Retrocopy TASIAAGRYVFPASTLGYARGVAAGMAPKARLAAYKVCW--VGG--CFDSDILAAFDAAVADGVDVVSLS

Parental  LGGDAGDYFADGLAIGSFHAVRHGIAVVCSAGNSGPAPGTVSNVAPWLFTAAASTMDREFPAYVVF-NDT
          .GG....Y..D..AIG.F.A...GI.V..SAGN.GP...TV.NVAPW..T..A..MDR.FPA.V...N..
Retrocopy VGGVVVPYYLDAIAIGAFGATEAGIVVSASAGNGGPGGLTVTNVAPWMATVGAGSMDRAFPANVQLGNGQ

Parental  KLKGQSLSASALSPASSSFPMI---DSSLAASPNRTQNESQLCFLGSLDPEKVKGKIVVCLRGVNPRVEK
          .L.G.S....................SS.AAS..........C..GSLDP..V.GKIVVC.RGVN.R..K
Retrocopy VLDGVSVYGGPALQSGKMYELVYAGASSGAASSAADGYSASMCLDGSLDPAAVRGKIVVCDRGVNSRAAK

Parental  GEAVLEAGGAGMVLANDVTTGNEIIADAHVLPATHIKFSDGQILFSYLKNT--KSPA-GTITRPETRLGT
          G..V..AGG.GMVLAN.V..G....AD.HVLPAT......G..L..Y........PA.GTI....T.LG.
Retrocopy GDVVHRAGGIGMVLANGVFDGEGLVADCHVLPATAVGAAAGDKLRKYIGSSTRQAPATGTILFEGTHLGV

Parental  KPAPFMAAFSSQGPNTVTPGILKPDITAPGVSVVAAWTRASAPTDLAFDKRRVAFNSESGTSMSCPHVAG
          .PAP..AAFS..GPN...P.ILKPD..APG....AAW.....P.....D.RR..FN..SGTSM.CPH..G
Retrocopy HPAPVVAAFSARGPNPQSPEILKPDLIAPGLNILAAWPSGVGPAGIPSDGRRTEFNILSGTSMACPHISG

Parental  VVGLLRTLRPDWSPAAIRSALMTTAVEVDNERHAILN-SSFAAANPFGFGAGHVSPARAMNPGLVYDLAA
          ...LL....P.WSPAAI.SALMTTA...DN........S....A..F.FGAGHV.P.RAM.PGLVYD...
Retrocopy LAALLKAAHPTWSPAAIKSALMTTAYIKDNSNGTMVDESTGVVADVFDFGAGHVDPMRAMDPGLVYDITP

Parental  VDYLNFLCSLRY
          VDY.NFLC.L.Y
Retrocopy VDYVNFLCNLNY

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_62 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	BGIOSGA006938	1 retrocopy	retro_oind_62 ,