RetrogeneDB ID: retro_oglu_27

Retrocopy location

• Organism: Oryza glumaepatula
• Coordinates: 6:8383356..8385132(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OGLUM06G10470
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OGLUM01G33050
• Aliases: None
• Description: None

Sequence

>retro_oglu_27
ATGGCCGCTAGAAGCGAGCTTCTCCGGCCGGCATTTGGTGAAGCATCTCCTTCGCTAGGGCGGTTTGTCATCAACCCTCA
CAGCTGCAGCTACAGGTGGTGGCACATGTTCCTGATCATGCTGGTGTTGTACTCGGCATGGGCATCGCCGTTCGAGCTGT
CCATGGAGAAGGCAGCCTCCATTGCTCTTGTTGTCACAGACCTGGTGGTCGATGTCTTCTTCGCCATTGACATTGCCTTA
TCTTTCTTCGTCGCATACCATGACACCTCCACCGGCCTCCTCATAACTGACTGCAGGAAGATCACAATGAGGTACCTGAA
ACGGCCGTGTTTCGCTCTGGATGTGGCCTCGACGATTCCTTTACAAATAATCTACCAGCTTGTGACTGGCAAAAGACAAG
GACTGTGGGGGCTCCTCAATCTTCTCCGTCTTTGGCGACTACGGCGCGTCAGCAAGCTCTTTGCGAGGGTGGAGAAGGAC
ATCAGATTCAACTATTTGTGGACCAGGCTTATCAAGCTCCTCTGTGTGACACTGTTTGCGCTGCATTTTGCCGCTTGCAT
CTACCTGTGGATGGCATTCAACTACAAGATCAAGGAGCTTACATGGATAGGCAGCCAGATCCATAGCTTTGAGGACCGAA
GCGTGTGGTTTTGCTACACCTGTGCAGTGTACTGGTCCATCACCACGCTTGCCACGGTCGGCTACGGTGACCTGCATGCC
ACCAACATTGGCGAGATGCTTTTCAGCATAGCCTTCATGCTTTTCAACATGGGCCTCACATCCTACATCATCGGCAACAT
CACCAACCTTGTTGTCCGTGAAACCTCCAACACCTTCAAGATGAGGGACATGGTGCAGCGGGTGTCGGAGTTTGTGAGCA
TGAACCGGCTGCCAGAGGCGATGAGGGAGCAGATGTTGGCTAGTGTGCAGCTCAGGTTCAGGACAGATGAGCAGTTGCAG
CAGGAGATGTTGTCAGAGCTGCCCAAAGCTGTGCGGTCGGGCGTCATGAAGCACCTGTTCAAGAGTGCTGTTGAGAGCTG
CTACCTATTCCAGGGAGTCTCCGATAGCCTCATTGTGCAGCTGGTCGCGGAGATGAAAGCAGAATTCTTTCCCCCCAAGG
CTAATGTTATCCTGGAGAATGAGACCTCGACGGACTGTTATATCATCATCTCCGGCGAAGTGGAGGCATTGACAACCCTT
GCAGATGGGACAGAGAAGCATGTGAAGAGAATAGGACCTCAGGGCATGGCAGGGGAAATCGGGGTGATGTTCAGCATTCC
GCAACCATTCACCATCCGGAGCAGGAGGCTCACCCAGGTTGTCCGCATAAGCCACATCCATCTGCTCCAGGCTGTCCAGC
CTAACACCGCAGATGGGTACATCGTGTTCTCCAATTTTATTCAGTACCTTGAGTCTCTGAAGGTGCAAACAAAGGATGTG
GCTTTTGTCAGCGATCATCTTTGGAATGGAAACTCAATGGTTTTGGAAAGGGCAACCGAGGTTGCTGTAGATGAATCAAA
AGAGGCCGCTCACAAAATGTTACCGTGCAAAGAACCCAAACGGGTTGTTATTCATGAGCAACTTCCCAACGCGACTAGCA
CAGCACTGCATCCTTCGCCGGGGAAGCTCGTCTTGCTCCCAGATTCGATGCAAGAACTGATGAAACTTTCAGAAAAGAAA
TTTGGGAAGGCCGTGAGAGGGATCCTCACTGTGGAAGGAGCAGAGGTCGAGGACATTGAAGTGATAAGAGATGGCGATCA
CCTGTTCTTTAGTTAG

Alignment

ORF - retro_oglu_27 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.09 %
• Parental protein coverage: 81.42 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RQALYGFLNLLRLWRLRRVSKLFARLEKDIRFSYLWTRLIKLLYVTLFAVHFASCIYLWMAFHHKAKELT
          RQ.L.G.LNLLRLWRLRRVSKLFAR.EKDIRF.YLWTRLIKLL.VTLFA.HFA.CIYLWMAF..K.KELT
Retrocopy RQGLWGLLNLLRLWRLRRVSKLFARVEKDIRFNYLWTRLIKLLCVTLFALHFAACIYLWMAFNYKIKELT

Parental  WIGSQFHGFEDRSVWFCYTCAVYWSITTLATVGYGDLHAANTGEMLFSIAFMLFNMGLTSYIIGNITNLV
          WIGSQ.H.FEDRSVWFCYTCAVYWSITTLATVGYGDLHA.N.GEMLFSIAFMLFNMGLTSYIIGNITNLV
Retrocopy WIGSQIHSFEDRSVWFCYTCAVYWSITTLATVGYGDLHATNIGEMLFSIAFMLFNMGLTSYIIGNITNLV

Parental  VHETANTFKMRDMVQRTSVFGRTNRLPVAMREQMMESLQLRFRAEEQLQQEMLSELPKAVRSGIAQHMFR
          V.ET.NTFKMRDMVQR.S.F...NRLP.AMREQM..S.QLRFR..EQLQQEMLSELPKAVRSG...H.F.
Retrocopy VRETSNTFKMRDMVQRVSEFVSMNRLPEAMREQMLASVQLRFRTDEQLQQEMLSELPKAVRSGVMKHLFK

Parental  GAVESCYLFQGVSDKLVLPLVAEMKAESFPPKADIILENEASTDCYIIVSGEVEVLTTLEDGTEKQVMRI
          .AVESCYLFQGVSD.L...LVAEMKAE.FPPKA..ILENE.STDCYII.SGEVE.LTTL.DGTEK.V.RI
Retrocopy SAVESCYLFQGVSDSLIVQLVAEMKAEFFPPKANVILENETSTDCYIIISGEVEALTTLADGTEKHVKRI

Parental  GPRGMAGEIGVMFNIPQPFTIRSRKLTQLVRISHSHMVQTIRPNTADGVVVFSNFVLYLESLKVKAKETA
          GP.GMAGEIGVMF.IPQPFTIRSR.LTQ.VRISH.H..Q...PNTADG..VFSNF..YLESLKV..K..A
Retrocopy GPQGMAGEIGVMFSIPQPFTIRSRRLTQVVRISHIHLLQAVQPNTADGYIVFSNFIQYLESLKVQTKDVA

Parental  FVRDHLRNGYSTVLGSATMFDVDESKESAHKMLPCKEPKRVSIHEHLLNGTGTALNGSSGKLVILPDSMQ
          FV.DHL.NG.S.VL..AT...VDESKE.AHKMLPCKEPKRV.IHE.L.N.T.TAL..S.GKLV.LPDSMQ
Retrocopy FVSDHLWNGNSMVLERATEVAVDESKEAAHKMLPCKEPKRVVIHEQLPNATSTALHPSPGKLVLLPDSMQ

Parental  DLMKLSEKKFGKAARGILTVGGAEVEDIEVIRDGDHLFFS
          .LMKLSEKKFGKA.RGILTV.GAEVEDIEVIRDGDHLFFS
Retrocopy ELMKLSEKKFGKAVRGILTVEGAEVEDIEVIRDGDHLFFS

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_27 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA004342	1 retrocopy	retro_oind_32,
Oryza brachyantha	OB01G37960	1 retrocopy	retro_obra_2,
Oryza barthii	OBART01G29050	1 retrocopy	retro_obar_20,
Oryza glumaepatula	OGLUM01G33050	1 retrocopy	retro_oglu_27 ,
Oryza nivara	ONIVA01G33130	1 retrocopy	retro_oniv_11,
Oryza rufipogon	ORUFI01G32100	1 retrocopy	retro_oruf_17,
Oryza sativa japonica	OS01G0718700	1 retrocopy	retro_osat_1,
Setaria italica	Si003861m.g	1 retrocopy	retro_sita_40,