RetrogeneDB ID: retro_obra_20

Retrocopy location

• Organism: Oryza brachyantha
• Coordinates: 1:31743714..31744881(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OB01G51450
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OB01G51480
• Aliases: None
• Description: None

Sequence

>retro_obra_20
ATGTGGGATGATGTGCATGCAGGGAAGAGCGGCGGCGTGCTGGAGGAGGACCCGGTGGGGAAGCTGAAGGTGTACGTGTA
CGAGATGCCCCGGAAGTACAACCTGAACCTGCTGGCGAAGGACAGCCGGTGCCTGCACCACATGTTCGCCGCCGAGATCT
TCATGCACCAGTTCCTCCTCTCCAGCGCCGTCAGGACGCTCGACCCGGAGGAGGCCGACTGGTTCTACACGCCGGCGTAC
ACCACCTGCGACCTCACGCCGCAGGGCTTCCCGCTCCCGTTCCGGGCGCCGCGCATCATGCGCAGCGCAGTCCACTACGT
CGCCACCACCTGGCCCTACTGGAACCGCACCGGCGGCGCCGACCACTTCTTCCTCGCGCCGCACGACTTCGGCGCCTGCT
TCCACTACCAGGAGGAGCGCGCCATCGAGCGCGGCGTCCTCCCCGTGCTCCGGCGGGCCACGCTGGTGCAGACGTTCGGG
CAGCGCAACCACCCGTGCCTCCAGGACGGCTCCATCACCATCCCGCCCTACGCCAACCCGCACAAGATGGAGGCGCACCT
CATCAGCCCGGCCACGCCGCGCTCCATCTTCGTCTACTTCCGGGGCCTCTTCTACGACATGGGCAACGACCCCGAGGGCG
GGTACTACGCCCGCGGCGCGCGCGCCGCCGTGTGGGAGAACTTCAAGGACAACCCGCTGTTCGACATCTCGACGGAGCAC
CCGGCGACGTACTACGAGGACATGCAGCGCGCCATCTTCTGCCTCTGCCCGCTTGGGTGGGCGCCCTGGAGCCCCCGCCT
GGTGGAGGCGGTGGTGTTCGGCTGCATCCCCGTCATCATCGCCGACGACATCGTGCTCCCCTTCGCCGACGCCATCCCCT
GGGAGCAGATCAGCGTGTTCGTCGCGGAGGAGGACGTGCCCAGGCTCGACTCCATCCTCGCCTCCATCCCGCTCGACGAC
GTCATCCGCAAGCAGCGCCTGCTGGCCAGCCCGGCCATGAAGCAGGCCGTGCTGTTCCACCAGCCGGCGAGGCCCGGCGA
CGCCTTCCACCAGATACTCAACGGCCTCGCGCGCAAGCTGCCGCACCGCAAGGACGTCTTCCTCGAGCCCGGCGACAGTG
GCGTCGACTGGAACCAGGGCCTCGAGAGCGACCTCAAGCCATGGTAG

Alignment

ORF - retro_obra_20 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.22 %
• Parental protein coverage: 92.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GSAGDVLEDDPVGRLKVYVYELPTKYNKKMVAKDSRCLSHMFAAEIFMHRFLLSSAIRTLNPEEADWFYT
          G..G.VLE.DPVG.LKVYVYE.P.KYN....AKDSRCL.HMFAAEIFMH.FLLSSA.RTL.PEEADWFYT
Retrocopy GKSGGVLEEDPVGKLKVYVYEMPRKYNLNLLAKDSRCLHHMFAAEIFMHQFLLSSAVRTLDPEEADWFYT

Parental  PVYTTCDLTPWGHPLPFKSPRIMRSAIQFISSHWPYWNRTEGADHFFVVPHDFGACFHYQEEKAIERGIL
          P.YTTCDLTP.G.PLPF..PRIMRSA.......WPYWNRT.GADHFF..PHDFGACFHYQEE.AIERG.L
Retrocopy PAYTTCDLTPQGFPLPFRAPRIMRSAVHYVATTWPYWNRTGGADHFFLAPHDFGACFHYQEERAIERGVL

Parental  PLLRRATLVQTFGQKDHVCLKEGSITIPPYAPPQKMKTHLVPPETPRSIFVYFRGLFYDTANDPEGGYYA
          P.LRRATLVQTFGQ..H.CL..GSITIPPYA.P.KM..HL..P.TPRSIFVYFRGLFYD..NDPEGGYYA
Retrocopy PVLRRATLVQTFGQRNHPCLQDGSITIPPYANPHKMEAHLISPATPRSIFVYFRGLFYDMGNDPEGGYYA

Parental  RGARASVWENFKNNPLFDISTDHPPTYYEDMQRSIFCLCPLGWAPWSPRLVEAVVFGCIPVIIADDIVLP
          RGARA.VWENFK.NPLFDIST.HP.TYYEDMQR.IFCLCPLGWAPWSPRLVEAVVFGCIPVIIADDIVLP
Retrocopy RGARAAVWENFKDNPLFDISTEHPATYYEDMQRAIFCLCPLGWAPWSPRLVEAVVFGCIPVIIADDIVLP

Parental  FADAIPWDEIGVFVAEDDVPKLDTILTSIPMEVILRKQRLLANPSMKQAMLFPQPAQPGDAFHQILNGLG
          FADAIPW..I.VFVAE.DVP.LD.IL.SIP.....RKQRLLA.P.MKQA.LF.QPA.PGDAFHQILNGL.
Retrocopy FADAIPWEQISVFVAEEDVPRLDSILASIPLDDVIRKQRLLASPAMKQAVLFHQPARPGDAFHQILNGLA

Parental  RKLPHDKSVYLSPGQKLLNWTQGPVGDLKPW
          RKLPH.K.V.L.PG.....W.QG...DLKPW
Retrocopy RKLPHRKDVFLEPGDSGVDWNQGLESDLKPW

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Oryza brachyantha was not studied using ChIP-Seq data.

EST

Oryza brachyantha was not studied using EST data.

TSS

Oryza brachyantha was not studied using FANTOM5 data.

Lab

retro_obra_20 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza brachyantha 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza longistaminata	KN538848.1_FG012	1 retrocopy	retro_olon_4,
Oryza brachyantha	OB01G51480	1 retrocopy	retro_obra_20 ,
Solanum tuberosum	PGSC0003DMG400014472	1 retrocopy	retro_stub_120,
Solanum lycopersicum	Solyc12g042360.1	1 retrocopy	retro_slyc_19,