RetrogeneDB ID: retro_osat_44

Retrocopy location

• Organism: Rice subsp. japonica (Oryza sativa japonica)
• Coordinates: 1:9018210..9019584(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OS01G0265000
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OS02G0744900
• Aliases: None
• Description: None

Sequence

>retro_osat_44
ATGGCCGCCGCCGTCGCCGCCGCCGCCTGCCACTCCCCGGCGCGCCTCGTGGTCACCTGCTCGAGCTCCGCCACGCCCGC
GCCGCCGCGGCGCCCGCTGCGGGTGGCCGTGGTGGGCGGCGGCCCCGCGGGCGCGTCGGCGGCCGAGGCGCTGGCGTCGG
CGGGCGCGCAGGCGTTCCTCCTCGAGCGCAACCCGTCGGGCGCCAAGCCCTGCGGCGGCGCCATCCCGCTCTGCATGCTC
GACGAGTTCGCCATCCCGCGTGACCTCGTCGACCGCCGCGTCACCCGCATGCGCGTCCTCTCGCCGTCCAACCTCGCCGC
CGACTTCTCCCGCGCGCTGCCCCCGGGCGCCCACATCCCCATGCTCCGCCGCGAGGTGCTCGACTCCTTCCTCCGCCGCC
GCGCCGCCGACGCCGGCGCCACCCTCGTCCCGGGCCTCGTCACCTCGCTCTCCCTCCCCGCCGACCCCGCCACCGACCCT
TACCTCGTCCACTACATCTCCTCCGACTCCGGTGGCCCCTCCTCCTCCCGGTGCGTCCTCGAGGTCGACGCCGTCATCGG
CGCGGACGGCGCCAACAGCCGTGTCGCCCGCGAGGTCGGCGCGGGGGACTACTCGACGGCCATCGCGTTCCAGGAGCGCA
TCCGCCTCCCCGACGAGGCCATGGCCTACTACGACGACCTCGCCGAGATGTACGTCGGCGGCGACGTCTCCCCGGACTTC
TACGGCTGGGTCTTCCCCAAGTGCGACCACGTCGCCGTCGGGACGGGCACGGTGGCCGCCAAGCCGGAGATCAAGAGGCT
CCAGTCGGGCATCCGCGCGCGCGCGGCGGGCAAGGTCGCCGGCGGCCGCGTGGTCAGGGTGGAGGCGCACCCGATCCCGG
AGCACCCGCGCCCCCGCCGCGTGGTGGGGCGCGTGGCGCTCGTCGGCGACGCGGCGGGCTACGTCACCCGGTGCTCCGGC
GAGGGCATCTACTTCGCGGCCAGGTCGGGGCGCCTCTGCGGCCGCGCCATGGCCGACGAGTGGCGGCTCACCGGCGCGGT
GACGGAGGCCGGGATACGGGCGGGATACCTCCGGCGGTGGGACGACGAGTTCCGCCCCACGTTCCGGTTCCTGGACCTGC
TGCAGCGGGTGTTCTACGGCGGGAACGCCGGGAGGGAGGCGCTGGTGGAGATGTGCGCCGACGAGCACGTGCAGCGCCGG
ACGTTCGACAGCTACCTGCACAAGCGGATGGCGCCCGCCGAGCCGTGGGGGGACCTCCGCCTGCTGTGGCGCACGGCGGC
GGCCATGGTGCGCTGCGGCGTGCTCGGCAGGGAGGTCGAGCGCCTCCGCCGTCTCGAGCAGCAGGCCGCCGACCAGGTGC
TCCTCCGCCATTGA

Alignment

ORF - retro_osat_44 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.64 %
• Parental protein coverage: 92.87 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ARLVTRAAASSPKLPSGRRLRVAVVGGGPAGGAAAEALAKGGVETVLIERKLDNCKPCGGAIPLCMVSEF
          ARLV.....S....P..R.LRVAVVGGGPAG..AAEALA..G....L.ER.....KPCGGAIPLCM..EF
Retrocopy ARLVVTCSSSATPAPPRRPLRVAVVGGGPAGASAAEALASAGAQAFLLERNPSGAKPCGGAIPLCMLDEF

Parental  DLPLDLVDRKVRKMKMISPSNVAVDIGGTLAPHEYIGMVRREVLDAYLRSRAEGAGAEVVNGLFLRYEAP
          ..P.DLVDR.V..M...SPSN.A.D....L.P...I.M.RREVLD..LR.RA..AGA..V.GL......P
Retrocopy AIPRDLVDRRVTRMRVLSPSNLAADFSRALPPGAHIPMLRREVLDSFLRRRAADAGATLVPGLVTSLSLP

Parental  KEP-NGSYVVHYNHYDSSNGKAGGEKRTFEVDAIVGADGANSRVAKDMGAGDYEYAIAFQERVKIPDDKM
          ..P....Y.VHY...DS..G.........EVDA..GADGANSRVA...GAGDY..AIAFQER...PD..M
Retrocopy ADPATDPYLVHYISSDS--GGPSSSRCVLEVDAVIGADGANSRVAREVGAGDYSTAIAFQERIRLPDEAM

Parental  KYYEERAEMYVGDDVSPDFYGWVFPKCDHVAVGTGTVTHKPDIKKFQAATRLRAKDRIEGGKIIRVEAHP
          .YY...AEMYVG.DVSPDFYGWVFPKCDHVAVGTGTV..KP.IK..Q...R.RA.....GG...RVEAHP
Retrocopy AYYDDLAEMYVGGDVSPDFYGWVFPKCDHVAVGTGTVAAKPEIKRLQSGIRARAAGKVAGGRVVRVEAHP

Parental  IPEHPRPKRVAGRVTLVGDAAGYVTKCSGEGIYFAAKSGRMCAEAIVAGSANGTRMVEESDLRR-YLAEF
          IPEHPRP.RV.GRV.LVGDAAGYVT.CSGEGIYFAA.SGR.C..A..A.....T..V.E...R..YL...
Retrocopy IPEHPRPRRVVGRVALVGDAAGYVTRCSGEGIYFAARSGRLCGRA-MADEWRLTGAVTEAGIRAGYLRRW

Parental  DRLYWPTYKVLDVLQKVFYRSNAAREAFVEMCADDYVQRMTFDSYLYKRVVPGNPLDDIKLAVNTIGSLV
          D....PT...LD.LQ.VFY..NA.REA.VEMCAD..VQR.TFDSYL.KR..P..P..D..L...T....V
Retrocopy DDEFRPTFRFLDLLQRVFYGGNAGREALVEMCADEHVQRRTFDSYLHKRMAPAEPWGDLRLLWRTAAAMV

Parental  RATALRREMEKV
          R...L.RE.E..
Retrocopy RCGVLGREVERL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Oryza sativa japonica was not studied using RNA-Seq expression data.

ChIP-Seq

Oryza sativa japonica was not studied using ChIP-Seq data.

EST

Oryza sativa japonica was not studied using EST data.

TSS

Oryza sativa japonica was not studied using FANTOM5 data.

Lab

retro_osat_44 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza sativa japonica 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 9 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Brachypodium distachyon	BRADI3G59430	1 retrocopy	retro_bdis_46,
Zea mays	GRMZM2G105644	1 retrocopy	retro_zmay_29,
Oryza meridionalis	OMERI02G30980	1 retrocopy	retro_omer_17,
Oryza nivara	ONIVA06G04710	1 retrocopy	retro_oniv_24,
Oryza punctata	OPUNC02G29860	1 retrocopy	retro_opun_22,
Oryza rufipogon	ORUFI02G34000	1 retrocopy	retro_oruf_42,
Oryza sativa japonica	OS02G0744900	1 retrocopy	retro_osat_44 ,
Sorghum bicolor	Sb04g028050	1 retrocopy	retro_sbic_27,
Triticum aestivum	Traes_6DL_0FF72D765	1 retrocopy	retro_taes_28,