RetrogeneDB ID: retro_oind_101

Retrocopy location

• Organism: Rice subsp. indica (Oryza sativa indica)
• Coordinates: AAAA02044296.1:739..1408(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BGIOSGA017090
• Aliases: None
• Description: None

Sequence

>retro_oind_101
GGCGAAGCCGATTTCTTTGCGTGCGGATTAAGTCTGGTGATTCACCCGAAAAATCCAATGGTTCCTACTGTCCACGCCAA
TTGGCGATATTTTGAAATGTACGACGAATCTGGAAAAGTAATCGAACAATGGTTCGGCGGCGGACAGGATTTAACGCCTT
ATTATTTGTTTGAAGAAGATGGCAAACATTTTCATCAAACCTGTAAAACCGCTTGCGACAAACACAATCCGGAATTTTAT
CCAAAATATAAAAAACAATGCGACTCGTATTTCTGGAACGCTCATAGAAATGAAGCCCGCGGACTTGGCGGTTTATTCTT
TGACTATTGCAAGGCAAATGAGCAAATGTCAATGGAAAACTGGTACGATTTTGTAACCGAAGTTGGAAACAGTTTCCTTG
AAGCCTACGTTCCGATTGTAGAAAAAAGAAAAAACTTAGAGTATACATCAGAAAACAGAAATTGGCAGGAAATCCGCCGT
GGCCGTTATGTTGAGTTTAATCTGGTTCATGATAAAGGAACTTTATTCGGCTTAAAAACCAACGGAAGAATCGAAAGTAT
TTTAATGAGTCTGCCTCCACATGTACAATGGGTTTACGATCATCATCCAGAAGCAGGAAGTGACGAAGAAAAATTAATTA
ATGTATTGCAGAATCCGATTGATTGGATT

Alignment

ORF - retro_oind_101 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.98 %
• Parental protein coverage: 55.89 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GPVPFFAAGISSVLHPKNPFAPTLHFNYRYFETDAPKDAPGAPRQWWFGGGTDLTPSYIIEEDVKHFHSV
          G...FFA.G.S.V.HPKNP..PT.H.N.RYFE.....D..G.....WFGGG.DLTP.Y..EED.KHFH..
Retrocopy GEADFFACGLSLVIHPKNPMVPTVHANWRYFEM---YDESGKVIEQWFGGGQDLTPYYLFEEDGKHFHQT

Parental  QKQACDKFDPSFYPRFKKWCDDYFYIKHRNERRGLGGIFFDDLNDYDQEMLLN---FATECADSVVPAYI
          .K.ACDK..P.FYP..KK.CD.YF...HRNE.RGLGG.FFD......Q....N...F.TE...S...AY.
Retrocopy CKTACDKHNPEFYPKYKKQCDSYFWNAHRNEARGLGGLFFDYCKANEQMSMENWYDFVTEVGNSFLEAYV

Parental  PIIERRKDTPFTEEHKAWQQLRRGRYVEFNLVYDRGTTFGLKTGGRIESILVSLPLTARWQYDHTPEEGT
          PI.........T.E...WQ..RRGRYVEFNLV.D.GT.FGLKT.GRIESIL.SLP....W.YDH.PE.G.
Retrocopy PIVXXXXXLEYTSENRNWQEIRRGRYVEFNLVHDKGTLFGLKTNGRIESILMSLPPHVQWVYDHHPEAGS

Parental  EERKLLDACINPKEWL
          .E.KL.....NP..W.
Retrocopy DEEKLINVLQNPIDWI

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_101 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.

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA017090	1 retrocopy	retro_oind_101 ,