RetrogeneDB ID: retro_oind_57

Retrocopy location

• Organism: Rice subsp. indica (Oryza sativa indica)
• Coordinates: 8:29470829..29471603(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BGIOSGA026518
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BGIOSGA026520
• Aliases: None
• Description: None

Sequence

>retro_oind_57
ATGGAGGCCGTAGCAGTGCACGCCAGCTTCTCGTCCTACTCCCCTCCGGTGGTCGCCGGCGGCCGCGACGACGCCGGCAG
CAGCAGGAGCATGTCCCGCCTGCCGGCTCGCGTCGCCGGCGCCGTAGCTCGCGGCATCGTCACCTTCGTCTTCGCCACAG
TGGGCACGATCCTGGGGGCGATCACCGGCGGGCTGATCGGGCTGGCGACGGAGAGCGGCATGGTGCGGGGCACCGGGATC
GGGGCCATCTCCGGCGCGGTGGTCGCCATGGAGGTCGTCGACTCCTCCGTCGCCATGTGGTGCTCCCACGACTCCGGGAT
CTGGAGCGTTCTCTACGTCCTTGACGTGATCTGGAGCCTCCTGACGGGGCGGCTGGTGCGGGAGAAGGTGGATCCGGCGG
TGCAGAACGCGGTGGACAGCCAGATGAACGCCGCCGACGCGCCCTTCAGGGAGAGCGCGCCGACGCTGGCGGAGATGTTC
GACACCGGCATCCCCGGCGTCGCCGCCGCCGCCACGGGCATGCCGGCGGACGCCATCGCCGCGCTCCCGGTCACCACGTT
CGCCGCCGCCGCCGGCGGCGACGACCGCGCCGGCTGCTCCGTGTGCCTCCAGGACTTGGAGGACGGCGAGCGGGCGCGGA
GGCTGCCGGAGTGCGGCCACACGTTCCACCTCCGCTGCATCGACAGCTGGCTGCTCAGGCACGCGTCGTGCCCCCTGTGC
CGGCGCACGGTGGTCGCCGCCGCCGTCGCCGTCGACGACGTCGTCGTCGGCTGA

Alignment

ORF - retro_oind_57 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.05 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEAVAVHASFSSYSPPVVAGGRDDAGSSRSMSRLPARVAGAVARGIVTFVFATVGTILGAITGGLIGLAT
          MEAVAVHASFSSYSPPVVAGGRDDAGSSRSMSRLPARVAGAVARGIVTFVFATVGTILGAITGGLIGLAT
Retrocopy MEAVAVHASFSSYSPPVVAGGRDDAGSSRSMSRLPARVAGAVARGIVTFVFATVGTILGAITGGLIGLAT

Parental  ESGMVRGTGIGAISGAVVAMEVVDSSVAMWCSHDSGIWSVLYVLDVIWSLLTGRLVREKVDPAVQNAVDS
          ESGMVRGTGIGAISGAVVAMEVVDSSVAMWCSHDSGIWSVLYVLDVIWSLLTGRLVREKVDPAVQNAVDS
Retrocopy ESGMVRGTGIGAISGAVVAMEVVDSSVAMWCSHDSGIWSVLYVLDVIWSLLTGRLVREKVDPAVQNAVDS

Parental  QMNAADAPFRESAPTLAEMFDTGIPGVAAAATGMPADAIAALPVTTFAAAAGGDDRAGCSVCLQDLEDGE
          QMNAADAPFRESAPTLAEMFDTGIPGVAAAATGMPADAIAALPVTTFAAAAGGDDRAGCSVCLQDLEDGE
Retrocopy QMNAADAPFRESAPTLAEMFDTGIPGVAAAATGMPADAIAALPVTTFAAAAGGDDRAGCSVCLQDLEDGE

Parental  RARRLPECGHTFHLHCIDSWLLRHASCPLCRRTVVA----VDDVVVG
          RARRLPECGHTFHL.CIDSWLLRHASCPLCRRTVVA....VDDVVVG
Retrocopy RARRLPECGHTFHLRCIDSWLLRHASCPLCRRTVVAAAVAVDDVVVG

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_57 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	BGIOSGA026520	1 retrocopy	retro_oind_57 ,