RetrogeneDB ID: retro_oind_21

Retrocopy location

• Organism: Rice subsp. indica (Oryza sativa indica)
• Coordinates: 9:8372862..8373930(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BGIOSGA030517
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BGIOSGA017925
• Aliases: None
• Description: None

Sequence

>retro_oind_21
ATGGCGGAGGTGTGCTGTGATTCTGCGGTGGTGGTCGGGGCGGAGGCGGAGGCGAGGGCGAGGGCGCGCGCCGGGAGGCG
GCGGCGGGCGGGAGTTGAGGGGGCAGGGAGGTGGAACGCCACGGCGACGGCTGCGGGTGTGGCGGCGGAGGAGGCCGCGA
CGAGGAAGCGGAGGGCGAGTGGTGGTGAGGCCGGGTTGGTGGTGGTGGCGAAGCGGCACGGGGCGGCGTCGGTCGCCGGG
AGGAGGAGGGAGATGGAGGACGCCGTGTCGCTGCGCGAGGCGTTCGCCGCGCCGGCGAACGGGGAGGTTGCGGCGGCGAG
GTGTGACTTCTACGGGGTGTTCGACGGGCACGGCTGCTCGCACGTGGCGGACGCGTGCAGGGAGCGGATGCACGAGCTCG
TCGCGGAGGAGATGGGCGCCGGGTCACCGGCGGCGGCGGCGCGCGAGCCGGCGTCTTGGACGGAGACGATGGAGCGGAGC
TTCGCGAGGATGGACGCCGAGGTGATCGCCGGCTGCCGAGCCGAGAGCGGCAGCTGCCGGTGCGAGGGGCAGAAGTGCGA
CCACGTGGGGTCCACCGCGGTGGTGGCCGTCGTGGAGGAGAGCCGCGTCGTCGTCGCCAACTGCGGCGACTCCCGCGCCG
TGCTCTGCCGCGGCGGCGCGCCCGTGCAGCTATCCGACCACAAGCCCGACCGCCCCGACGAGCTGGAGCGGATCGAGGCG
GCCGGCGGCCGCGTCATCTTCTGGGAGGGCGCCCGTGTCCTCGGCGTCCTCGCCATGTCGCGCTCCATCGGCGACGCCTA
CCTGAAGCCCTACGTCACCGCCGTGCCGGAGGTGACGGTGACCGGCAGGTCGGACTTCGACGAGTGCCTCATCCTCGCCA
GCGACGGCCTCTGGGACGTCGTCAGCAACGAGGCCGCGTGCGAGGTGGCGCAGTCGTGCCTCCGCCGCGGCAGGCAGCGG
TGGTGCGCCGAGGCGGCGGCGGTGCTGACCAAGCTGGCCCTCGCTCGCCGCAGCTCCGACAACATCTCTGTCGTCGTCGT
CGATCTCCGGCGAGGCAACGCCTTGTAG

Alignment

ORF - retro_oind_21 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.66 %
• Parental protein coverage: 69.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AGVARCGKRQRVA-GARAGAGAATAGPCRPSAGAGFGSRWWPRYGVTSVFGRRREMEDAVSIRPDFL---
          AGV...G.....A..A...A..A.....R.S.G.........R.G..SV.GRRREMEDAVS.R..F....
Retrocopy AGVEGAGRWNATATAAGVAAEEAATRKRRASGGEAGLVVVAKRHGAASVAGRRREMEDAVSLREAFAAPA

Parental  RGSTSSGKHHFFGVFDGHGCSHVARMCQDRMHELVVDAYKKAVSGKEAAAAAPA-WKDVMEKGFARMDDE
          .G........F.GVFDGHGCSHVA..C..RMHELV............AAA..PA.W...ME..FARMD.E
Retrocopy NGEVAAARCDFYGVFDGHGCSHVADACRERMHELVAE--EMGAGSPAAAAREPASWTETMERSFARMDAE

Parental  ATIWAKSRTGGEPACRCELQTPARCDHVGSTAVVAVVGPNRVVVANSGDSRAVLCRAGVPVPLSVDHKPD
          .........G....CRCE.Q....CDHVGSTAVVAVV...RVVVAN.GDSRAVLCR.G.PV.LS.DHKPD
Retrocopy VIAGCRAESG---SCRCEGQ---KCDHVGSTAVVAVVEESRVVVANCGDSRAVLCRGGAPVQLS-DHKPD

Parental  RPDELERIKAAGGRVIYWDGARVLGVLAMSRAIGDGYLKPYVTSEPEVTVTERADDDECLILASDGLWDV
          RPDELERI.AAGGRVI.W.GARVLGVLAMSR.IGD.YLKPYVT..PEVTVT.R.D.DECLILASDGLWDV
Retrocopy RPDELERIEAAGGRVIFWEGARVLGVLAMSRSIGDAYLKPYVTAVPEVTVTGRSDFDECLILASDGLWDV

Parental  VTNEMACEVVRACFR
          V.NE.ACEV...C.R
Retrocopy VSNEAACEVAQSCLR

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_21 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA017925	1 retrocopy	retro_oind_21 ,
Oryza glumaepatula	OGLUM05G20150	1 retrocopy	retro_oglu_4,
Oryza meridionalis	OMERI05G16600	1 retrocopy	retro_omer_16,
Oryza nivara	ONIVA05G19940	1 retrocopy	retro_oniv_23,
Oryza glaberrima	ORGLA05G0165000	1 retrocopy	retro_ogla_36,
Oryza rufipogon	ORUFI05G20280	1 retrocopy	retro_oruf_40,