RetrogeneDB ID: retro_obar_24

Retrocopy location

• Organism: Oryza barthii
• Coordinates: 8:15513496..15514957(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OBART08G15210
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OBART02G31860
• Aliases: None
• Description: None

Sequence

>retro_obar_24
ATGGCGGCGGCGACGACAATGTGCGCCGCGGTGGCGGTGCTCCTCGTTCTGACGTCGACAATGGCGGCCGCCGCCGGCGA
TGGCGATGGCGATGGCGGTGGCTTCGACTACAAGAAGGCGCTGCACAGCGGGCTGCTCTACTTCGAGGCGCAGCGGTCGG
GGCACCTGCCGTACAACCAGCGGGTGCGGTGGCGCGGCCACTCGGGGCTCGCCGACGGGCTGCAGCAAGGGGTGGACCAC
GTGCTGGAGGCCATCAAGTGGGGCACCGACTACCTCGTGAAGGCGCACACCGCCGCCGACGAGCTGTGGGCCGAGGTCGG
CGACGGCGACACCGACCACTACTGCTGGCAGCGGCCGGAGGACATGACGACGTCGAGGCAGGCCTACAAGGTGGACCGCG
ACAACCCCGGCTCCGACGTCGCCGGCGAGACCGCCGCCGCGCTCGCCGCCGCGTCCATCGTGTTCCGCCGCTCCAACCCC
CGCTACTCCCGCCTCCTCCTCCGCCACGCCGAGCAGCTGTTCGACTTCGGCGACAGGTACAGGGGCAAGTACGACAGCAG
CATCGGCGAGGTGAGGGCGTACTACGCGTCGGTGAGCGGCTACGGCGACGAGCTGCTGTGGGCGGCGCTGTGGCTGCACC
GCGCCACCGGCCGCCGCGGCTACCTCGACTACGCCGTCGCCATGGCCGACGAGCTCGGCGGCGTCGGCTGGGCCGTCACC
GAGTTCAGCTGGGACGTCAAGTACGCCGGCCTCCAGATCCTCGCCGCCAAGGTGCTCATGGACGGCGGCGACCACCCGGC
GGCGCACGCGGCGACGCTGGAGCAGTACAGGTCCAAGGCGGAGCACTACCTCTGCGCCTGCCTCGGCAAGAACGCCGCCG
CCGGCGACAACGTCAACCGCACCGCCGGCGGCATGCTGTTCGTCCGCCGCTGGAACAACATGCAGTACGTCACCAACGCC
GCCTTCCTCCTCACCGTCTACTCCCGCTACCTCCGCGACTCCGGCGGCGACACCATCCGGTGCTCCGGTGGGGCTATGGC
AACCGACGACGAGTTGGCGGCGATGGCGAGGGCGCAGGCGGACTACGTGCTGGGCGACAACCCGGCGGGGGTGAGCTACA
TGGTCGGGTACGGGCGGCGGTTCCCGCGGCGGGTGCACCACCGCGGGGCGTCCATGGTGTCGCACCGCGCGGACGGGCGG
TTCGTGGGGTGCGTGCAGGGGTACGACCGCTGGTTCCGGCGCGGCGGCGCGAACCCGAACGTGGTCGCCGGAGCCATCGT
CGGCGGGCCGGACGACCGCGACAGGTTCAGGGACAGCCGCGACAACTACATGCAGACGGAAGCGTGCACGTACAACACCG
CGCCCATGGTCGGCGTCTTCGCGCACCTGCACGCCCAGAAGATGGCGGCGAGGACTGCTAATAATAATGCCGATCGATCG
ATGATTAAACGAGTGGATTGA

Alignment

ORF - retro_obar_24 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.06 %
• Parental protein coverage: 69.8 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  HALEAIKWGTDYFIKAHTKPNELWAEVGDGDTDHYCWQRPEDMTTSRQAYKVDRERPGSDVAGETAAAMA
          H.LEAIKWGTDY..KAHT...ELWAEVGDGDTDHYCWQRPEDMTTSRQAYKVDR..PGSDVAGETAAA.A
Retrocopy HVLEAIKWGTDYLVKAHTAADELWAEVGDGDTDHYCWQRPEDMTTSRQAYKVDRDNPGSDVAGETAAALA

Parental  AASIVFRKSNPHYASLLLHHAQQLFEFADKYRGKYDSSIAEVKSYYASVSGYKDELLWAALWLHRATGKA
          AASIVFR.SNP.Y..LLL.HA.QLF.F.D.YRGKYDSSI.EV..YYASVSGY.DELLWAALWLHRATG..
Retrocopy AASIVFRRSNPRYSRLLLRHAEQLFDFGDRYRGKYDSSIGEVRAYYASVSGYGDELLWAALWLHRATGRR

Parental  HYLDYVVDNADCFGGTGWAITEFSWDVKYAGVQILAARLLL-RGEHEERHRSTLEQYRAKAEHYVCGCLG
          .YLDY.V..AD..GG.GWA.TEFSWDVKYAG.QILAA..L...G.H...H..TLEQYR.KAEHY.C.CLG
Retrocopy GYLDYAVAMADELGGVGWAVTEFSWDVKYAGLQILAAKVLMDGGDHPAAHAATLEQYRSKAEHYLCACLG

Parental  RNADGGADANVERSPGGMLYVRQWNNMQYVTNAAFLLAAYADYLGDDADGAVSCAGGETAGAGEVAALAR
          .NA..G...NV.R..GGML.VR.WNNMQYVTNAAFLL..Y..YL.D.......C.GG..A...E.AA.AR
Retrocopy KNAAAG--DNVNRTAGGMLFVRRWNNMQYVTNAAFLLTVYSRYLRDSGGDTIRCSGGAMATDDELAAMAR

Parental  AQVDYVLGTNPRGISYLVGYGAKYPNRVHHRAASIVPYKHSKEFIGCTQGFDHWFGRRSSNPNVLVGAIV
          AQ.DYVLG.NP.G.SY.VGYG...P.RVHHR.AS.V.......F.GC.QG.D.WF.R...NPNV..GAIV
Retrocopy AQADYVLGDNPAGVSYMVGYGRRFPRRVHHRGASMVSHRADGRFVGCVQGYDRWFRRGGANPNVVAGAIV

Parental  GGPDRRDRFRDNRENYMQTEACTYNTAPMVGMFAKLN
          GGPD.RDRFRD.R.NYMQTEACTYNTAPMVG.FA.L.
Retrocopy GGPDDRDRFRDSRDNYMQTEACTYNTAPMVGVFAHLH

Legend:

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

Expression

RNA-Seq

Oryza barthii was not studied using RNA-Seq expression data.

ChIP-Seq

Oryza barthii was not studied using ChIP-Seq data.

EST

Oryza barthii was not studied using EST data.

TSS

Oryza barthii was not studied using FANTOM5 data.

Lab

retro_obar_24 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza barthii 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA009019	1 retrocopy	retro_oind_14,
Oryza barthii	OBART02G31860	1 retrocopy	retro_obar_24 ,
Oryza glaberrima	ORGLA02G0273700	1 retrocopy	retro_ogla_39,
Oryza rufipogon	ORUFI02G33530	1 retrocopy	retro_oruf_46,
Oryza sativa japonica	OS02G0738600	1 retrocopy	retro_osat_30,