RetrogeneDB ID: retro_oind_55

Retrocopy location

• Organism: Rice subsp. indica (Oryza sativa indica)
• Coordinates: AAAA02048606.1:104..938(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BGIOSGA040253
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BGIOSGA016143
• Aliases: None
• Description: None

Sequence

>retro_oind_55
ATGGGCATGAGCGACTTCTACTCCACCGGCGCCGATCGGCAGGAAGCCATCGCCACGCTGCACCGGGCGCTGGAGCTGGG
CGTCACGCTGCTCGACACCGCCGACATGTATGGCCCGCACACCAACGAAGAGCTGGTGGGGGAAGCGATCAAAGGCAAGC
GGCAACAGGTGTTCCTGGCCACCAAGTTCGGCATCCTGCGCGATCCGGCGGATCCTTCGGCGCGCGGCGTCAGCAGCCGC
CCCGAGTATATCCGGCGCTCCGTCGAGGGCAGCCTGCGGCGCTTGGGCGTGGAGGAGATCGATCTTTATTATCAGCACCG
GGTCGATCCGCAGGTGCCGATCGAGGACGTCGTCGGCACGATGGCGGATCTGATCCGCGAAGGCAAGATCCGCCACATCG
GCCTGAGCGAGGCGTCGGTCGCCACGCTGGAGCGGGCGCAAAAGGTGCATCCGATCACCGCGCTGCAGACCGAATATTCG
CTGTGGACGCGCGACGCCGAGCAGGGCGTGCTGGCGGCCTGCGAGCGCCTGGGCATCGGCTTTGTGCCCTACAGCCCGCT
AGGGCGCGGTTTCCTCACCGGCGCTATCCAGCGGCCGGAGGATCTGGCCGAGGACGACTTCCGCCGCAGCAACCCGCGCT
TCCAGGGGGAAAACTTCAGTCGCAATCTGGCGCTGGTGGAGAAGGTGAGCGAGCTGGCGGCGCAGAAGGGCGTTAAACCT
TCGCAGCTGGCGCTGGCCTGGGTGTTGGCGCAGGGGGAACACATCGTGCCGATCCCCGGCACCAAACGCCGTCGTTACCT
GGAAGAGAACGTCGCGGCGGCGGAGATACGCTGA

Alignment

ORF - retro_oind_55 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.88 %
• Parental protein coverage: 78.35 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGMSAFYGPPKPEPDMVALIHHAVAAGVTLLDTSDIYGPHTNELLLGKALQGGVRDKVELATKFGIA---
          MGMS.FY..........A..H.A...GVTLLDT.D.YGPHTNE.L.G.A..G..R..V.LATKFGI....
Retrocopy MGMSDFYSTGADRQEAIATLHRALELGVTLLDTADMYGPHTNEELVGEAIKGK-RQQVFLATKFGILRDP

Parental  FEDGKRGVRGDPAYVRAACEGSLRRLGVDSIDLYYQHRVDKKVPIEVTIGELKKLVEEGKIKYIGLSEAS
          .....RGV...P.Y.R...EGSLRRLGV..IDLYYQHRVD..VPIE...G....L..EGKI..IGLSEAS
Retrocopy ADPSARGVSSRPEYIRRSVEGSLRRLGVEEIDLYYQHRVDPQVPIEDVVGTMADLIREGKIRHIGLSEAS

Parental  ASTIRRAHAVHPITAVQLEWSLWSRDVEEDIIPTCRELGIGIVAYSPLGRGFFSAGAKLVESLSDQDFRK
          ..T..RA..VHPITA.Q.E.SLW.RD.E......C..LGIG.V.YSPLGRGF........E.L...DFR.
Retrocopy VATLERAQKVHPITALQTEYSLWTRDAEQGVLAACERLGIGFVPYSPLGRGFLTGAIQRPEDLAEDDFRR

Parental  HIPRFQQENLEKNAEIFERVNAMAARKGCTPSQLALAWVHHQGSDVCPIPGTTKIENLNQNIGALSVK
          ..PRFQ.EN...N....E.V...AA.KG..PSQLALAWV..QG....PIPGT.....L..N..A....
Retrocopy SNPRFQGENFSRNLALVEKVSELAAQKGVKPSQLALAWVLAQGEHIVPIPGTKRRRYLEENVAAAEIR

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_55 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA016143	1 retrocopy	retro_oind_55 ,
Solanum lycopersicum	Solyc09g097970.2	1 retrocopy	retro_slyc_103,