RetrogeneDB ID: | retro_oind_20 | ||
Retrocopy location | Organism: | Rice subsp. indica (Oryza sativa indica) | |
| Coordinates: | AAAA02045927.1:2059..2773(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | BGIOSGA039930 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | BGIOSGA006950 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_oind_20
ATGATTGCGTACGGCGATGCAGATGCTATGGTTGCGGGTGGTGCAGAAAAAGCCAGTACCCCTCTGGGTGTCGGTGGTTT
TGGTGCAGCGCGTGCGCTCTCTACCCGTAACGATAATCCTCAGGCGGCAAGCCGTCCGTGGGATAAAGACCGTGACGGTT
TCGTACTGGGTGACGGTGCGGGCATGCTCGTGCTGGAAGAGTACGAACACGCGAAAAAACGCGGCGCGAAAATTTATGCT
GAAGTCGTTGGCTTTGGTATGAGTAGCGATGCTTATCACATGACGTCTCCTCCGGAGAATGGCGCAGGTGCTGCGCTGGC
AATGGAAAACGCGATCCGTGATGCGGGCATTACGCCAGCTCAGATTGGCTACGTGAACGCGCACGGTACCTCTACACCTG
CAGGCGACAAAGCGGAAGCTCAGGCTGTTAAGTCTATCTTCGGCGAGTCTGCCAGCCGCGTACTGGTCAGCTCCACAAAA
TCCATGACCGGTCACCTGTTGGGTGCGGCGGGTGCAGTAGAGTCAATCTACTCTATCCTTGCGCTGCGCGATCAGGCGGT
TCCACCAACCATCAACCTGGATAACCCGGATGAAGGTTGCGATCTGGACTTCGTGCCTCACGAAGCGCGTCAGGTTAGCG
GTATGGAGTACACCCTGTGTAACTCCTTCGGCTTCGGCGGTACCAATGGCTCGCTGATTTTCAAACGCGTGTAA
ORF - retro_oind_20 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 53.59 % |
| Parental protein coverage: | 50.43 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MIQFGDADVMVAGGTESSIDALSIAGFSRLRALSTKYNSLPQAASRPFDCGRDGFVIGEGCGVMVLEALD |
| MI..GDAD.MVAGG.E.....L...GF...RALST..N..PQAASRP.D..RDGFV.G.G.G..VLE... | |
| Retrocopy | MIAYGDADAMVAGGAEKASTPLGVGGFGAARALSTR-NDNPQAASRPWDKDRDGFVLGDGAGMLVLEEYE |
| Parental | HAKERGAKIYAEVRGYGMSGDAHHITQPQNDGRGATLAMKRALDQSGLQADQIDYLNAHATSTPLGDAVE |
| HAK.RGAKIYAEV.G.GMS.DA.H.T.P...G.GA.LAM..A....G....QI.Y.NAH.TSTP.GD..E | |
| Retrocopy | HAKKRGAKIYAEVVGFGMSSDAYHMTSPPENGAGAALAMENAIRDAGITPAQIGYVNAHGTSTPAGDKAE |
| Parental | ANAIKSVFGDHATSGGLALSSTKGAIGHLLGAAGSVEAIFTVLAIHHGIAPPTLNLEKPDTLFEGAFMPL |
| A.A.KS.FG..A.......SSTK...GHLLGAAG.VE.I...LA......PPT.NL..PD......F.P. | |
| Retrocopy | AQAVKSIFGESASR--VLVSSTKSMTGHLLGAAGAVESIYSILALRDQAVPPTINLDNPDEGCDLDFVPH |
| Parental | SSPKKMPIRAAISNSFGFGGTNTSLLF |
| .............NSFGFGGTN.SL.F | |
| Retrocopy | EARQVSGMEYTLCNSFGFGGTNGSLIF |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
Oryza sativa indica was not studied using RNA-Seq expression data.
Oryza sativa indica was not studied using ChIP-Seq data.
Oryza sativa indica was not studied using EST data.
Oryza sativa indica was not studied using FANTOM5 data.
retro_oind_20 was not experimentally validated.
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.Parental genes homology:
Parental genes homology involve 1 parental gene, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Oryza sativa indica | BGIOSGA006950 | 2 retrocopies |
retro_oind_2, retro_oind_20 ,
|