RetrogeneDB ID: retro_oind_58

Retrocopy location

• Organism: Rice subsp. indica (Oryza sativa indica)
• Coordinates: CH399799.1:2551..3433(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BGIOSGA039178
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BGIOSGA026004
• Aliases: None
• Description: None

Sequence

>retro_oind_58
ATGTCGATCCTCATCAACAAAGACACCAAGGTCATCACCCAAGGTATCACCGGCAAGACCGGCCAGTTCCACACCCGCAT
GTGCCGCGACTACGCGAATGGCAAGAATGCCTTCGTCGCTGGCGTGAACCCGAAGAAGGCCGGTGAAGACTTCGAAGGCA
TCCCCATCTATGCCAACGTCACCGAAGCCAAGAACGCCACCGGCGCCACCGTCTCGGTGATCTACGTGCCGCCCGCCGGC
GCTGCTGCCGCCATCTGGGAAGCCGTCGAAGCCGAGCTGGACCTGGCCATCTGCATCACCGAAGGCATCCCCGTGCGTGA
CATGCTGGCTCTGAAGGACCGCATGGCCAAGGCCGGTTCCAAGACCCTGCTGCTGGGCCCGAACTGCCCCGGCCTGATCA
CCCCGGACGAAATCAAGATCGGCATCATGCCGGGTCACATCCACAAGAAGGGCCGCATCGGCGTGGTCTCCCGTTCGGGC
ACCCTGACCTATGAAGCCGTGGGCCAGCTGACCGCCCTGGGCCTGGGCCAGTCCTCCGCCGTCGGTATCGGTGGCGACCC
GATCAACGGTCTGAAGCACATTGACGTCATGAAGGCCTTCAACGACGATCCGGACACCGACGCCGTCATCATGATCGGTG
AAATCGGTGGCCCTGACGAAGCCAACGCCGCCCGTTGGATCAAGGACAACATGAAGAAGCCGGTGGTTGGCTTCATCGCC
GGTGTGACCGCGCCCCCGGGCAAGCGCATGGGCCACGCAGGCGCGCTGATCTCCGGCGGTGCCGACACTGCCGAAGCCAA
GCTGGCCATCATGGAAGAGTGCGGCATCAAGGTTACCCGCAACCCGTCCGAAATGGGTCGCCTGCTGAAGTCGGTGCTGT
AA

Alignment

ORF - retro_oind_58 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.89 %
• Parental protein coverage: 58.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KPGCVGGVTPKKGGTEHLGLPVFNSVAEAKAETKANASVIYVPPPFAAAAIMEAMEAELDLVVCITEGIP
          K...V.GV.PKK.G....G.P....V.EAK..T.A..SVIYVPP..AAAAI.EA.EAELDL..CITEGIP
Retrocopy KNAFVAGVNPKKAGEDFEGIPIYANVTEAKNATGATVSVIYVPPAGAAAAIWEAVEAELDLAICITEGIP

Parental  QHDMVKVKAALNKQ-SKTRLIGPNCPGIIKPGECKIGIMPGYIHKPGRVGIVSRSGTLTYEAVFQTTAVG
          ..DM...K....K..SKT.L.GPNCPG.I.P.E.KIGIMPG.IHK.GR.G.VSRSGTLTYEAV.Q.TA.G
Retrocopy VRDMLALKDRMAKAGSKTLLLGPNCPGLITPDEIKIGIMPGHIHKKGRIGVVSRSGTLTYEAVGQLTALG

Parental  LGQSTCVGIGGDPFNGTNFVDCLEKFVDDPQTEGIVLIGEIGGTAEEDAAAFIQESKTQKPVVAFIAGLT
          LGQS..VGIGGDP.NG....D....F.DDP.T.....IGEIGG..E..AA..I......KPVV.FIAG.T
Retrocopy LGQSSAVGIGGDPINGLKHIDVMKAFNDDPDTDAVIMIGEIGGPDEANAARWIKDN-MKKPVVGFIAGVT

Parental  APPGRRMGHAGAIVSGGKGTAQDKIKALREAGVTVVESPAKIG
          APPG.RMGHAGA..SGG..TA..K.....E.G..V...P...G
Retrocopy APPGKRMGHAGALISGGADTAEAKLAIMEECGIKVTRNPSEMG

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_58 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	BGIOSGA026004	1 retrocopy	retro_oind_58 ,