RetrogeneDB ID: retro_oind_34

Retrocopy location

• Organism: Rice subsp. indica (Oryza sativa indica)
• Coordinates: AAAA02042192.1:2452..3454(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BGIOSGA039299
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BGIOSGA007628
• Aliases: None
• Description: None

Sequence

>retro_oind_34
ATGACCATCAAGATCGGTATCAACGGCTTCGGCCGCATCGCCCGCAACGTGCTGCGCTCGGCCGTGCAGAACTTCAGCGA
CATCGAAGTCGTGGGCATCAACGACCTGCTGGAGCCCGACTACCTGGCCTACATGCTGCAGTACGACTCGGTGCACGGCC
GCTTCGAGGGCACCGTGTCGGTCGAGGGCAACACGCTGGTGGTGAACGGCAAGAAGATCCGCCTGACGCAGGAGCGCGAT
CCGGCCGCCCTGAAGTGGGGCGAGATCGGCGCCGAGGTGGTGATCGAGTCCACGGGCCTGTTCCTCGACAAGACGACGGC
CCAGAAGCACCTGGACGCGGGCGCGAAGAAGGTCGTGCTGTCGGCGCCGTCGAAAGACGACACGCCGATGTTCGTCTATG
GCGTGAACCACGACACGTACGCCGGCCAGGCCATCATCTCCAACGCCTCGTGCACCACCAACTGCCTGGCCCCCGTGGCC
AAGGTGCTCAACGACAAGTGGGGCATCAAGCGCGGCCTGATGACCACGGTGCACGCCGCCACGGCCACGCAGAAGACGGT
GGACGGCCCCTCCAACAAGGACTGGCGCGGCGGCCGCGGCATCCTGGAGAACATCATCCCCTCCTCCACCGGCGCCGCCA
AGGCCGTGGGCGTGGTGATTCCCGCGCTGAACAAGAAGCTGACCGGCATGTCCTTCCGCGTGCCCACCTCCGACGTGTCG
GTGGTGGACCTGACGGTGGAGCTGGAGAAGGCCGCCACGTACGAAGAGATCAAGGCCGAGATGAAGGCCCAGTCCGAAGG
CGCCCTGAAGGGCGTGCTGGGCTACACGGAAGACAAGGTGGTGGCCACTGACTTCCGCGGCGACGCCCGCACATCCATCT
TCGACGCCGATGCCGGCATCGCGCTGGACGGCACCTTCGTGAAGGTCGTCTCCTGGTACGACAACGAGTGGGGCTACTCC
AACAAGTGCCTGGAAATGGTGCGCGTGGTCGCGGGCAAGTAA

Alignment

ORF - retro_oind_34 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.54 %
• Parental protein coverage: 80.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KVGINGFGRIGRLVLRIATSR-DDIEVVAVNDPFIDAKYMAYMFKYDSTHGPFKGSIKVVDDSTLEINGK
          K.GINGFGRI.R.VLR.A.....DIEVV..ND......Y.AYM..YDS.HG.F.G...V....TL..NGK
Retrocopy KIGINGFGRIARNVLRSAVQNFSDIEVVGIND-LLEPDYLAYMLQYDSVHGRFEGTVSV-EGNTLVVNGK

Parental  KVTITSKRDPADIPWGNFGAEYVVESSGVFTTTEKASAHLKGGAKKVVISAPSA-DAPMFVVGVNEKSYD
          K...T..RDPA...WG..GAE.V.ES.G.F.....A..HL..GAKKVV.SAPS..D.PMFV.GVN...Y.
Retrocopy KIRLTQERDPAALKWGEIGAEVVIESTGLFLDKTTAQKHLDAGAKKVVLSAPSKDDTPMFVYGVNHDTYA

Parental  PKMNVVSNASCTTNCLAPLAKVVHEEFGIVEGLMTTVHATTATQKTVDGPSMKDWRGGRGAAQNIIPSST
          ......SNASCTTNCLAP.AKV.....GI..GLMTTVHA.TATQKTVDGPS.KDWRGGRG...NIIPSST
Retrocopy GQA-IISNASCTTNCLAPVAKVLNDKWGIKRGLMTTVHAATATQKTVDGPSNKDWRGGRGILENIIPSST

Parental  GAAKAVGKVLPELNGKLTGMAFRVPTPNVSVVDLTCRIEKSASYDDVKAAIKAASEGALKGILGYTDEDV
          GAAKAVG.V.P.LN.KLTGM.FRVPT..VSVVDLT...EK.A.Y...KA..KA.SEGALKG.LGYT...V
Retrocopy GAAKAVGVVIPALNKKLTGMSFRVPTSDVSVVDLTVELEKAATYEEIKAEMKAQSEGALKGVLGYTEDKV

Parental  VSNDFVGDARSSIFDAKAGIGLSSSFMKLVSWYDNEWGYSNRVLDLIAHMA
          V..DF.GDAR.SIFDA.AGI.L...F.K.VSWYDNEWGYSN..L......A
Retrocopy VATDFRGDARTSIFDADAGIALDGTFVKVVSWYDNEWGYSNKCLEMVRVVA

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_34 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA007628	1 retrocopy	retro_oind_34 ,
Triticum aestivum	Traes_6AS_D1274A812	1 retrocopy	retro_taes_64,