RetrogeneDB ID: retro_obar_20

Retrocopy location

• Organism: Oryza barthii
• Coordinates: 6:7221709..7223485(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OBART06G09660
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OBART01G29050
• Aliases: None
• Description: None

Sequence

>retro_obar_20
ATGGCCGCTAGAAGCGAGCTTCTCCGGCCGGCATTTGATGAAGCATCTCCTTCGCTAGGGCGGTTTGTCATCAACCCTCA
TAGCTGCAGCTACAGGCGGTGGCACATGTTCCTGATCATGCTAGTGTTGTACTCGGCATGGGCATCGCCGTTCGACCTGT
CCATGGAGAAGGCAGCCTCCATTGCTCTTGTTGTCACGGACCTGGTGGTCGATGTCTTCTTCGCCATTGACATTGCCTTA
TCTTTCTTCGTCGCATACCATGACACCTCCACCGGCCTCCTCATAACTGACTGCAGGAAGACCACAATGAGGTACCTGAA
ACGGCCGTGTTTCGCTCTGGATGTGGCCTCGATGATTCCTTTACAAATAATCTACCAGCTTGTGACTGGCAAAAGACAAG
GACTTTGGGGGCTCCTCAATCTTCTCCGTCTTTGGCGACTACGGCGTGTCAGCAAGCTCTTTGCAAGGGTGGAGAAGGAC
ATCAGATTCAACTATTTGTGGACCAGGCTTATCAAGCTTCTATGTGTGACACTGTTTGCGCTGCATTTTGCCGCTTGCAT
CTACCTGTGGATGGCATTCAACTACAAGATCAAGGAGCTTACATGGATAGGCAACCAGATCCATAGCTTTGAGGACCGAA
GCGTGTGGTTTTGCTACACCTGTGCAGTGTACTGGTCCATCACCACGCTTGCCACGGTCGGCTACGGTGACCTGCATGCC
ACCAACATTGGTGAGATGCTTTTCAGCATAGCCTTCATGCTTTTCAACATGGGCCTCACATCCTACATCATCGGCAACAT
CACCAACCTCGTTGTCCGTGAAACCTCCAACACCTTCAAGATGAGGGACATGGTGCAGCGGGTGTCGGAGTTTGTGAGCA
TGAACCGGCTGCCAGAGGCGATGAGGGAGCATATGTTGGCCAGCGTGCAGCTCAGGTTCAGGACAGATGAGCAGCTGCAG
CAGGAGATGTTGTCAGAGCTGCCCAAAGCTGTGCGGTCGGGCATCATGAAGCACCTGTTCAAGAGTGCTGTTGAGAGCTG
CTACCTATTCCAGGGAGTCTCCGATAGCCTCATTGTGCAGCTGGTCGCGGAGATGAAAGCAGAATTCTTTCCCCCCAAGG
CTAATGTTATCCTGGAGAATGAGACCTCGACGGACTGTTATATCATCATCTCCGGCGAAGTGGAGGCATTGACAACCCTT
GCAGATGGGACAGAGAGGCATGTGAAGAGAATAGGACCTCAGGGCATGGCAGGGGAAATCAGGGTGATGTTCAGCATTCC
GCAACCATTCACCATCCGGAGCAGGAGGCTTACCCAGGTTGTCCGCATAAGCCACATCCATCTGCTCCAGGCTGTCCAGC
CTAACACCGCAGATGGGTACATCGTGTTCTCCAATTTTATTCAGTACCTTGAGTCTCTGAAGGTGCAAACAAAGGATGTG
GCTTTTGTCAGCGATCATCTTTGGAATGGAAACTCAATGGTTTTGGAAAGGGCAACCGAGGTTGCTGTAGATGAATCAAA
AGAGGCCTCTCACAAAATGTTACCGTGCAAAGAACCCAAACGGGTTGTTATTCATGAGCAACTTCCCAACGCGACTAGCA
CAGCACTGCATCCTTCGCCGGGGAAGCTCGTCTTGCTCCCAGATTCGATGCAAGAACTGATGAAACTTTCAGAACAGAAA
TTTGGGAAGGCCGTGAGAGGGATCCTCACTGTGGAAGGAGCCGAGGTCGAGGACATTGAAGTGATAAGAGATGGCGATCA
CCTGTTTTTTAGTTAG

Alignment

ORF - retro_obar_20 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.98 %
• Parental protein coverage: 83.36 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LLMIYRIVSGKRQALYGFLNLLRLWRLRRVSKLFARLEKDIRFSYLWTRLIKLLYVTLFAVHFASCIYLW
          L..IY..V.GKRQ.L.G.LNLLRLWRLRRVSKLFAR.EKDIRF.YLWTRLIKLL.VTLFA.HFA.CIYLW
Retrocopy LQIIYQLVTGKRQGLWGLLNLLRLWRLRRVSKLFARVEKDIRFNYLWTRLIKLLCVTLFALHFAACIYLW

Parental  MAFHHKAKELTWIGSQFHGFEDRSVWFCYTCAVYWSITTLATVGYGDLHAANTGEMLFSIAFMLFNMGLT
          MAF..K.KELTWIG.Q.H.FEDRSVWFCYTCAVYWSITTLATVGYGDLHA.N.GEMLFSIAFMLFNMGLT
Retrocopy MAFNYKIKELTWIGNQIHSFEDRSVWFCYTCAVYWSITTLATVGYGDLHATNIGEMLFSIAFMLFNMGLT

Parental  SYIIGNITNLVVHETANTFKMRDMVQRTSVFGRTNRLPVAMREQMMESLQLRFRAEEQLQQEMLSELPKA
          SYIIGNITNLVV.ET.NTFKMRDMVQR.S.F...NRLP.AMRE.M..S.QLRFR..EQLQQEMLSELPKA
Retrocopy SYIIGNITNLVVRETSNTFKMRDMVQRVSEFVSMNRLPEAMREHMLASVQLRFRTDEQLQQEMLSELPKA

Parental  VRSGIAQHMFRGAVQSCYLFQGVSDKLVLPLVAEMKAESFPPKADIILENEASTDCYIIVSGEVEVLTTL
          VRSGI..H.F..AV.SCYLFQGVSD.L...LVAEMKAE.FPPKA..ILENE.STDCYII.SGEVE.LTTL
Retrocopy VRSGIMKHLFKSAVESCYLFQGVSDSLIVQLVAEMKAEFFPPKANVILENETSTDCYIIISGEVEALTTL

Parental  EDGTEKQVMRIGPRGMAGEIGVMFNIPQPFTIRSRKLTQLVRISHSHMVSTIRPNTADGVVVFSNFVLYL
          .DGTE..V.RIGP.GMAGEI.VMF.IPQPFTIRSR.LTQ.VRISH.H......PNTADG..VFSNF..YL
Retrocopy ADGTERHVKRIGPQGMAGEIRVMFSIPQPFTIRSRRLTQVVRISHIHLLQAVQPNTADGYIVFSNFIQYL

Parental  ESLKVKAKETAFVRDHLRNGYSTVLGSATMFDVDESKESAHKMLPCKEPKRVSIHEHLLNGTGTALNGSS
          ESLKV..K..AFV.DHL.NG.S.VL..AT...VDESKE..HKMLPCKEPKRV.IHE.L.N.T.TAL..S.
Retrocopy ESLKVQTKDVAFVSDHLWNGNSMVLERATEVAVDESKEASHKMLPCKEPKRVVIHEQLPNATSTALHPSP

Parental  GKLVILPDSMQDLMKLSEKKFGKAARGILTVGGAEVEDIEVIRDGDHLFFS
          GKLV.LPDSMQ.LMKLSE.KFGKA.RGILTV.GAEVEDIEVIRDGDHLFFS
Retrocopy GKLVLLPDSMQELMKLSEQKFGKAVRGILTVEGAEVEDIEVIRDGDHLFFS

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_20 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.

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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,