RetrogeneDB ID: retro_oind_102

Retrocopy location

• Organism: Rice subsp. indica (Oryza sativa indica)
• Coordinates: AAAA02044643.1:2554..3154(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BGIOSGA031928
• Aliases: None
• Description: None

Sequence

>retro_oind_102
TCAAAATTATATATCGTTCCAACGCCAATTGGCAATCTTGAAGACATGACTTTTAGAGCCATTCGGGTTTTAAAAGAAGT
AGATTTGATTTTGGCTGAAGACACCCGAACAAGCGGTAAACTCTTAAAGCATTTTGAAATTGGCACGCACATGCACAGCC
ATCACATGCACAACGAGCATAAAACTACCGAAAATTTAATTGCAAGATTAAAAGCCGGCGAGACCATCGCTTTAATTTCA
GATGCTGGAACACCAGCTATTTCAGATCCTGGATTTTTGCTGACACGTGCTTGTGTAGAAAATAAAATTGAAGTAGAATG
TCTTCCGGGTGCAACGGCTTTTGTTCCCGCTCTTGTAAACAGCGGACTTCCAAATGACAAATTTGTTTTTGAAGGTTTTC
TGCCTGATAAAAAAGGACGTCAGACTCGTTTTTTGGCTTTAGCCGAAGAAACCAGAACCATGATTTTATACGTTTCTCCG
CATAAACTCGTTAAAACTTTAGCCGAATTTGTGCAGTATTTTGGAGAAGACAGACAAGTCTGCGTTTCGAGAGAATTATC
AAAATTACACGAAGAAAATATGCGCGGAACAGCAAAAGAA

Alignment

ORF - retro_oind_102 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.25 %
• Parental protein coverage: 60.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SGLYLVATPIGNLEDITLRALRILKCADVILSEDTRHSGKLLQHYNIKTPLLSFHKFNEREREPNILKRL
          S.LY.V.TPIGNLED.T.RA.R.LK..D.IL.EDTR.SGKLL.H..I.T...S.H..NE.....N...RL
Retrocopy SKLYIVPTPIGNLEDMTFRAIRVLKEVDLILAEDTRTSGKLLKHFEIGTHMHSHHMHNEHKTTENLIARL

Parental  HEGEAVALISDAGTPGISDPGMELARLCATEGIPVIPIPGPSAAIAALSASGLPTDEFTFVGFLPKHARS
          ..GE..ALISDAGTP.ISDPG..L.R.C....I.V...PG..A...AL..SGLP.D.F.F.GFLP.....
Retrocopy KAGETIALISDAGTPAISDPGFLLTRACVENKIEVECLPGATAFVPALVNSGLPNDKFVFEGFLP-DKKG

Parental  RKERLEISACQAATQIFYVPPHGIHQFLSDAASSFGDSRSCVIAREITKLHEEFWRGTIGE
          R..R....A....T.I.YV.PH.....L......FG..R.....RE..KLHEE..RGT..E
Retrocopy RQTRFLALAEETRTMILYVSPHKLVKTLAEFVQYFGEDRQVCVSRELSKLHEENMRGTAKE

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_102 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	BGIOSGA031928	1 retrocopy	retro_oind_102 ,