RetrogeneDB ID: retro_oind_26

Retrocopy location

• Organism: Rice subsp. indica (Oryza sativa indica)
• Coordinates: 1:28943295..28943760(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BGIOSGA004088
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BGIOSGA036765
• Aliases: None
• Description: None

Sequence

>retro_oind_26
ATGCAGATCTTCGTGAAGACCCTGACGGGGAAGACCATCACGCTGGAGGTGGAGAGCAGCGACACGATCCAGAACGTCAA
GGCGAAGGTGCAGGACAAGGAGGGGATCCCGCCGGACCAGCAGCGGCTCATCTTCGCCGGCAAGCAGCTGGAGGACGGGC
GCACGCTGGCCGACTACAACATCCAGAAGGAGTCGACGCTGCACCTGGTGCTCCGCCTCCGCGGCGGCCTGAACGTCAAG
GTGAGGACGCTCACCGGCAAGGAGATCGACATCGACATCGAGATGACGGACACGGTGGACAGGATCAAGGAGCGCGTCGA
GGAGAGGGAGGGCATCCCGCCCGTGCAGCAGAGGCTCATCTACGGCGGGAAGCAGCTTGCCGACGACAAGACGGCGCACG
ACTACAAGATCGAGGCTGGCTCCGTCCTCCACCTCGTCCTCGCTCTCCGAGGCGGGAACTTCTGA

Alignment

ORF - retro_oind_26 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.79 %
• Parental protein coverage: 99.35 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLV
          MQIFVKTLTGKTITLEVESSDTI.NVKAK.QDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLV
Retrocopy MQIFVKTLTGKTITLEVESSDTIQNVKAKVQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLV

Parental  LRLRGGTMIKVKTLTGKEIEIDIEPTDTIDRIKERVEEKEGIPPVQQRLIYAGKQLADDKTAKDYNIEGG
          LRLRGG...KV.TLTGKEI.IDIE.TDT.DRIKERVEE.EGIPPVQQRLIY.GKQLADDKTA.DY.IE.G
Retrocopy LRLRGGLNVKVRTLTGKEIDIDIEMTDTVDRIKERVEEREGIPPVQQRLIYGGKQLADDKTAHDYKIEAG

Parental  SVLHLVLALRGG
          SVLHLVLALRGG
Retrocopy SVLHLVLALRGG

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_26 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA036765	1 retrocopy	retro_oind_26 ,
Musa acuminata	GSMUA_Achr3G30150_001	1 retrocopy	retro_macu_90,
Oryza glaberrima	ORGLA06G0191700	1 retrocopy	retro_ogla_18,