RetrogeneDB ID: retro_oglu_18

Retrocopy location

• Organism: Oryza glumaepatula
• Coordinates: 1:27445672..27447937(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OGLUM01G27350
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OGLUM06G01450
• Aliases: None
• Description: None

Sequence

>retro_oglu_18
ATGGGCGAGGGCGAGTTCGTCGACGTCGAGCGCGGCGTGGTCGCTGAGGGGGCGTTGGACGACGACGCGTCGCCGATCGA
GGAGGTCCGGCTGACGGTTCCGGTCACTGACGACCCGTCCCTTCCGGTGTGGACGTTCCGGATGTGGACACTCGGCCTGC
TCTCGTGCGTGCTCATGAGCTTCCTGAACCAGTTCTTCTCCTACCGCACCGAGCCGCTCATCGTCACCCAGATCACCGTG
CAGGTGGCCTCGCTGCCTCTGGGCCACATCCTCGCCCGCGTGCTGCCGCGCCGCAAGTTCAAGGCCCCCGCGCTGCTCGG
CGGCGGGGAGTGCAGCCTCAACCCGGGGCCCTTCAACATGAAGGAGCACGTGCTCGTCTCCATCTTCGCCAACGCCGGCT
GCGCCTTCGGCAGCGGGTCCGCCTACGCCGTCATGATCGTCGACATCATCCGCGCCTTCTACGGGCGGTCCATCTCCTTC
TTCCCCGCATGGCTCCTCATCACCACCACGCAGGTGCTCGGCTACGGGTGGGCGGGGCTGATGCGCAAGTACGTGGTGGA
GCCGGCGCAAATGTGGTGGCCCGGCACGCTCGTGCAGGTGTCGCTGTTCAGGGCGCTGCACGGGAAGGGGGAAGAGGAGG
AGAATACGGAGGGCAGCGGCGGCGGGATGTCTCAGGCCAAGTTCTTCCTGATCGCGCTCGCCTGCAGCTTCCTGTGGTAC
GCCGTGCCGGGTTACCTGTTCCCGACGCTGACCTCCGTCTCGTGGGTCTGCTGGATCTTCTCCAAGTCCGTCACCGCGCA
GCAGCTGGGCTCCGGCATGAAGGGCCTGGGCCTCGGCGCCTTCACCCTCGACTGGACGGCCGTGTCAGCCTTCCTGTACA
GCCCGCTGATCTCGCCGTTCTTTGCCACCGCCAACATCTTGGCCGGCTACGTGCTCCTGATGTACGTGGTCGTGCCGGTG
TCGTACTGGGGCCTCGACCTGTACAACGCCCGGAGGTTCCCCATCTTCTCGTCGCACCTGTTCACGGCCACCGGCAGCAC
ATACGACATCACGGCCATCGTGAACGACCGCTTCGAGATCGACATGGACGGGTACCATCGGATGGGGCGGATCAACATGA
GCACGTTCTTCGCGCTGTCCTACGGGCTCGGCTTCGCGACGATCGCGGCCACCGTCACGCACGTGGCGCTGTTCCACGGG
AAGGAGATCTACCGCCGGTTCCGCGCGTCGCAGAGGGACAAGCCCGACGTGCACACGAGGCTGATGAAGAGCTACCGCGA
CGTGCCGAGCTGGTGGTTCTACGCGATGCTCGCGCTGTCCATGGCCGTCTCGCTCTTGCTCTGCACCGTCCTCAGGTCGG
CGGTGCAGCTCCCGTGGTGGGGTCTCCTCTTCGCCTGCGCCATGGCCTTCGTGTTCACGCTGCCGATCAGCATCATCACG
GCCACGACCAACCAGACGCCGGGGCTCAACATCATCACCGAGTACGTCATCGGGCTCATGCTTCCGGGCAAGCCCATCGC
CAACGTCTGCTTCAAGGCGTACGGCTACATGAGCATGTCGCAGGCCGTGTCCTTCCTGTCCGACTTCAAGCTCGGCCACT
ACATGAAGATACCCCCCAAGTCCATGTTCCTCGTGCAGTTGGTCGGCACGGTGGTCGCCTCCACGGTCAACCTCGTGGTG
GCGTACTGGCTGCTGGGTTCCATCCCCAACATCTGCCAGGACGCGCTCCTCCCGGCGGATAGCCCGTGGACGTGCCCGAA
CGACCGCGTCTTCTTCGACGCGTCCGTCATCTGGGGCCTCGTCGGGCCGCGCCGCATCTTCGGGCCACTCGGGAACTACG
GCGCGCTCAATTGGTTCTTCCTCGCTGGCGCCGTGGGACCCGTCATTGTGTACTTGCTCCACAGGGCGTTCCCCAGCAAG
ACCTGGATACCGATGATCAACCTGCCGGTGCTCATCGGAGCGACCTCCTACATGCCGCCGGCGACGGCCGTGAACTACAA
CTCGTGGCTGATCATCGGGATCATCTTCAACTTCTTCGTTTTCCGGTACAGGAAGCTGTGGTGGAAGAGGTACAACTACA
TCCTCTCGGCTGCGCTCGACGCCGGCGTCGCGTTCATGGCGGTGCTGCTCTACTTCTCGCTGTCGATGGAGAACAGGAGC
ATCAGCTGGTGGGGTACGGCCGGCGAGCACTGCCCGCTGGCCTCATGCCCTACCGCCAAAGGGATAAACTTGGGCGCTGA
TAGCGTCTGCCCTGTTGTGTTATAA

Alignment

ORF - retro_oglu_18 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.41 %
• Parental protein coverage: 73.64 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VVDDQVLGFGWAGIFRRYLVEPAAMWWPSNLVQVSLFRALH---EKEARSKG---GLTRNQFFLVAFICS
          ....QVLG.GWAG..R.Y.VEPA.MWWP..LVQVSLFRALH...E.E....G...G.....FFL.A..CS
Retrocopy ITTTQVLGYGWAGLMRKYVVEPAQMWWPGTLVQVSLFRALHGKGEEEENTEGSGGGMSQAKFFLIALACS

Parental  FAYYIFPGYLFQMLTSLSWICWVFPHSVLAQQLGSGLSGLGIGAIGLDWSTVSSYLGSPLASPWFATANV
          F..Y..PGYLF..LTS.SW.CW.F..SV.AQQLGSG..GLG.GA..LDW..VS..L.SPL.SP.FATAN.
Retrocopy FLWYAVPGYLFPTLTSVSWVCWIFSKSVTAQQLGSGMKGLGLGAFTLDWTAVSAFLYSPLISPFFATANI

Parental  AAGFFFIMYIITPIAYW-FNFYKAQNFPIFSDGLFTSTGQKYNISSIVDSHFHFDTKAYEKNGPLYLSTF
          .AG....MY...P..YW....Y.A..FPIFS..LFT.TG..Y.I..IV...F..D...Y...G....STF
Retrocopy LAGYVLLMYVVVPVSYWGLDLYNARRFPIFSSHLFTATGSTYDITAIVNDRFEIDMDGYHRMGRINMSTF

Parental  FAVTYGVGFASLTATIVHVLLFHGSEIWQLSKSAFQEKRMDIHTKLMRRYKQVPEWWFVCILIANIAVTI
          FA..YG.GFA...AT..HV.LFHG.EI......A.Q....D.HT.LM..Y..VP.WWF...L....AV..
Retrocopy FALSYGLGFATIAATVTHVALFHGKEIYRRFR-ASQRDKPDVHTRLMKSYRDVPSWWFYAMLALSMAVSL

Parental  FACEYYIEQLQLPWWGVLLACAIAFFFTLPIGIITATTNQTPGLNIITEYIMGYLYPGRPVANMCFKVYG
          ..C.......QLPWWG.L.ACA.AF.FTLPI.IITATTNQTPGLNIITEY..G...PG.P.AN.CFK.YG
Retrocopy LLCTVLRSAVQLPWWGLLFACAMAFVFTLPISIITATTNQTPGLNIITEYVIGLMLPGKPIANVCFKAYG

Parental  YISMSQALTFLQDFKLGHYMKIPPRTMFMAQVVGTLIAAFVYIGTAWWLMETIPNICNTELLPSDSPWTC
          Y.SMSQA..FL.DFKLGHYMKIPP..MF..Q.VGT..A..V....A.WL...IPNIC...LLP.DSPWTC
Retrocopy YMSMSQAVSFLSDFKLGHYMKIPPKSMFLVQLVGTVVASTVNLVVAYWLLGSIPNICQDALLPADSPWTC

Parental  PGDHVFYDASVIWGLISPRRIFGDLGTYSAVNWFFLGGAIAPILVWFAHKAFPNQNWIMLINMPVLIGAT
          P.D.VF.DASVIWGL..PRRIFG.LG.Y.A.NWFFL.GA..P..V...H.AFP...WI..IN.PVLIGAT
Retrocopy PNDRVFFDASVIWGLVGPRRIFGPLGNYGALNWFFLAGAVGPVIVYLLHRAFPSKTWIPMINLPVLIGAT

Parental  GQMPPATAVNYTTWILVGFLSGYVVYRYRRDWWERHNYLLSGALDAGLAFMAVLIYLCLGLENISLNWWG
          ..MPPATAVNY..W...G......V.RYR..WW.R.NY.LS.ALDAG.AFMAVL.Y..L..EN.S..WWG
Retrocopy SYMPPATAVNYNSWLIIGIIFNFFVFRYRKLWWKRYNYILSAALDAGVAFMAVLLYFSLSMENRSISWWG

Parental  NDLDGCPLASCPTAKGV
          .....CPLASCPTAKG.
Retrocopy TAGEHCPLASCPTAKGI

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Oryza glumaepatula was not studied using ChIP-Seq data.

EST

Oryza glumaepatula was not studied using EST data.

TSS

Oryza glumaepatula was not studied using FANTOM5 data.

Lab

retro_oglu_18 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza glumaepatula 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza glumaepatula	OGLUM06G01450	1 retrocopy	retro_oglu_18 ,
Oryza rufipogon	ORUFI06G01440	1 retrocopy	retro_oruf_39,