RetrogeneDB ID: retro_oniv_11

Retrocopy location

• Organism: Indian wild rice (Oryza nivara)
• Coordinates: 6:8307453..8309229(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ONIVA06G11180
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ONIVA01G33130
• Aliases: None
• Description: None

Sequence

>retro_oniv_11
ATGGCCGCTAGAAGCGAGCTTCTCCGGCCAGCATTTGGTGAAGCATCTCCTTCGCTAGGACGGTTTGTCATCAACCCTCA
CAGCTGCAGCTACAGGTGGTGGCACATGTTCCTGATCATGCTGGTGTTGTACTCGGCATGGGCATCGCCATTCGAGCTGT
CCATGGAGAAGACAGCTTCCATTGCTCTTGTTGTCACAGACCTGGTGGTCGATGTCTTCTTCGCCATTGACATTGCCTTA
TCCTTCTTCGTCGCATACCGTGACACCTCCACCGGCCTCCTCATAACTGACCGCAGGAAGATCACAATGAGGTACCTGAA
ACGGCCGTGTTTCGCTCTAGATGTGGCCTCGACGATTCCTTTACAAATAATCTACCAGCTTGTGACTGGCAAAAGACAAG
GACTGTGGGGGCTCCTCAATCTTCTCCGTCTTTGGCGACTACGGCGCGTCAACAAGCTCTTTGCGAGGGTGGAGAAAGAC
ATCAGATTCAACTATTTGTGGACCAGGCTTATCAAGCTCCTCTGTGTGACACTGTTTGCGCTGCATTTTGCCGCTTGCAT
CTACCTGTGGATGGCATTCAACTACAAGATCAAGGAACTTACATGGATAGGTAGCCAGATCCATAGCTTTGAGGACCGAA
GCGTGTGGTTTTGCTACACCTGTGCAGTGTACTGGTCCATCACCACGCTTGCCACGGTCGGCTACGGTGACCTGCATGCC
ACCAACATTGGCGAGATGCTTTTCAGCATAGTCTTCATGCTTTTCAACATGGGCCTCACATCCTACATCATCGGCAACAT
CACTAACCTCGTTGTCCGTGAAACCTCCAACACCTTCAAGATGAGGGACATGGTGCAGCGGGTGTCGGAGTTCGGGAGCA
TGAACCGGCTGCCAGAGGCGATGAGGGAGCAGATGTTGGCCAGCGTGCAGCTCAGGTTCAGGACAGATGAGCAGCTACAG
CAGGAGATGTTGTCAGAGCTGCCCAAGGCTGTGCGGTCGAGCGTCATGAAGCACATGTTCAAGAGTGCTATCGAGAGCTG
CTACCTATTCCAGGGAGTCTCCGACAGCCTCATTGTGCAGCTGGTCGCGGAGATGAAAGCAGAATTCTTCCCCCCCAAGG
CTAATGTTATCCTGGAGAATGAGACCTCGACGGACTGTTATATTATCATCTCTGGCGAAGTGGAGGCATTGACAACCCTT
GCAGATGGGACAGAGAAGCATGTGAAGAGAATAGGACCTCGGGGCATGGCAGGGGAAATCGGGGTGATGTTCAGCATTCC
GCAGCCATTCACCATCCGGAGCATGAGCCTCACCCATGTTGTCCGCATAAGCCATATCCATCTGCTCCAGGCTGTCCGGC
CTAACACCGCAGATGGGTACATCGTGTTCTTCAATTTTATTCAGTACCTTGAGTCTCTGAAGGTGCAAACAAAGGATGTG
GCTTTTGTCAGCGATCATCTTTGGAATGGAAACTCAATGGTTTTGGGAAGGGCAACCGAGGTTGCTGTAGATGAATCAAA
AGAGGCCGCTCACAAAATGTTACCGTGCAAAGAACCCAAACGGGTTGTTATTCATGAGCAACTTCCCAACGCGACTAGCA
CAACACTCCATCCTTCGCCTGGGAAGCTCGTCTTACTCCCAGATTCGATGCAAGAACTGATGAAACTTTCAGAAAAGAAA
TTTGGGAAGGCCGTGAGAGGGATCCTCACTGTGGAAGGAGCCGAGGTCGAGGACATTGAAGTGATAAGAGATGGCGATCA
CCTGTTCTTTAGTTAG

Alignment

ORF - retro_oniv_11 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.0 %
• Parental protein coverage: 78.77 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RQALYGFLNLLRLWRLRRVSKLFARLEKDIRFSYLWTRLIKLLYVTLFAVHFASCIYLWMAFHHKAKELT
          RQ.L.G.LNLLRLWRLRRV.KLFAR.EKDIRF.YLWTRLIKLL.VTLFA.HFA.CIYLWMAF..K.KELT
Retrocopy RQGLWGLLNLLRLWRLRRVNKLFARVEKDIRFNYLWTRLIKLLCVTLFALHFAACIYLWMAFNYKIKELT

Parental  WIGSQFHGFEDRSVWFCYTCAVYWSITTLATVGYGDLHAANTGEMLFSIAFMLFNMGLTSYIIGNITNLV
          WIGSQ.H.FEDRSVWFCYTCAVYWSITTLATVGYGDLHA.N.GEMLFSI.FMLFNMGLTSYIIGNITNLV
Retrocopy WIGSQIHSFEDRSVWFCYTCAVYWSITTLATVGYGDLHATNIGEMLFSIVFMLFNMGLTSYIIGNITNLV

Parental  VHETTNTFKMRDMVQRTSVFGRTNRLPVAMREQMMESLQLRFRAEEQLQQEMLSELPKAVRSGIAQHMFR
          V.ET.NTFKMRDMVQR.S.FG..NRLP.AMREQM..S.QLRFR..EQLQQEMLSELPKAVRS....HMF.
Retrocopy VRETSNTFKMRDMVQRVSEFGSMNRLPEAMREQMLASVQLRFRTDEQLQQEMLSELPKAVRSSVMKHMFK

Parental  GAVQSCYLFQGVSDKLVLPLVAEMKAESFPPKADIILENEASTDCYIIVSGEVEVLTTLEDGTEKQVMRI
          .A..SCYLFQGVSD.L...LVAEMKAE.FPPKA..ILENE.STDCYII.SGEVE.LTTL.DGTEK.V.RI
Retrocopy SAIESCYLFQGVSDSLIVQLVAEMKAEFFPPKANVILENETSTDCYIIISGEVEALTTLADGTEKHVKRI

Parental  GPRGMAGEIGVMFNIPQPFTIRSRKLTQLVRISHSHMVSTIRPNTADGVVVFSNFVLYLESLKVKAKETA
          GPRGMAGEIGVMF.IPQPFTIRS..LT..VRISH.H.....RPNTADG..VF.NF..YLESLKV..K..A
Retrocopy GPRGMAGEIGVMFSIPQPFTIRSMSLTHVVRISHIHLLQAVRPNTADGYIVFFNFIQYLESLKVQTKDVA

Parental  FVRDHLRNGYSTVLGSATMFDVDESKESAHKMLPCKEPKRVSIHEHLLNGTGTALNGSSGKLVILPDSMQ
          FV.DHL.NG.S.VLG.AT...VDESKE.AHKMLPCKEPKRV.IHE.L.N.T.T.L..S.GKLV.LPDSMQ
Retrocopy FVSDHLWNGNSMVLGRATEVAVDESKEAAHKMLPCKEPKRVVIHEQLPNATSTTLHPSPGKLVLLPDSMQ

Parental  DLMKLSEKKFGKAARGILTVGGAEVEDIEVIRDGDHLFFS
          .LMKLSEKKFGKA.RGILTV.GAEVEDIEVIRDGDHLFFS
Retrocopy ELMKLSEKKFGKAVRGILTVEGAEVEDIEVIRDGDHLFFS

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Oryza nivara was not studied using ChIP-Seq data.

EST

Oryza nivara was not studied using EST data.

TSS

Oryza nivara was not studied using FANTOM5 data.

Lab

retro_oniv_11 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza nivara 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,