RetrogeneDB ID: retro_oind_65

Retrocopy location

• Organism: Rice subsp. indica (Oryza sativa indica)
• Coordinates: 5:20046090..20048478(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BGIOSGA018122
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BGIOSGA027162
• Aliases: None
• Description: None

Sequence

>retro_oind_65
ATGGCGGCGAGCGATGATGGCCAGCTCAGGACGTGGGTCTCCGACCGCCTCATGGCGCTCCTCGGATACTCCCAGGGCCT
CGTGGCGCGGCTCGTCGTCCGCCTCGCGCGGGAGTGCGCCTCCGCGGGTGACCTCGCGGCGCGGCTCGTCGACCTCGCCG
GGTTCCCGCCTTCCCCCGACACCGCCGCGTTCGCCGAGGACGTGTACGGGAGGGTGCCCCGCAGTTGCGGCGGCGGCGGC
GACGACGCCGGGGTCAGCGAGTACCAGAGGCAGATGCAGGAGGCTGCGGCGATGGCCAAGAAGCAGAGCACCATCAAGCT
GCTCGACGACGACGGCGAGATCGGCGTTTCCGCGTCGCCCTCCAGCGGCGGCAGGAAGCGTTTCAGGAGGAAGGCCGTGG
GCGAAGACGATGACGATGCCGGACGGAACGCGCGACGGCGGCGTAGCCCGGACGACGAGGAGGAGGACGGCGACGCCGGC
GAGGAAGAAGAGATGGAGCGGGATCAGATCGAGAGGGCGCAGCTCGAGCGGAACATCAGGGAGCGCGACGCGGCGAGCAC
GAGGAGGCTGACGGATCGGAAGACGACCAAGCGGGAGCAGGGCGAGCTCGCGCGCCGGTCGGACGCCATGGACAAGAACG
ACACCTCGGGGCTCAGGAGGCTCTCCCGGCGCGCGTACCTGCAGAGGCGGAAGGAGAAGAAGGTCGAGGAGATGCGCGAC
GAGATCGTCGACCACGAGTTCCTCTTCCCCGGCGTCCAGCTGACGGCCGCCGAGGAGAGGGACATGAGGCACAAGAAGCA
AGTCTACGGCCTCGTGCACGATCGCGACGACTACTACAGAATGCCGGACGCCTACGACGCCGCCGCGAACGTCGATCAGG
AGAAGAGGTTCTCGGTGGCGCGGCGGCGGTACGAGGAGCCAGCTGAGGCGGCGAGGGACGGCAAGACGGCGAACGCCTTG
TCCGAGCAGGAGGCCTGGGAGGAGCAGCAGATACGGAAGTCGAGGCTGCAGTTCGGATCCATGGATCGCGGCCGGCGCGG
CGACGAGTACGAGCTCCTGTTCGACGACGGCGTCGAGTTCGTCAGGTCGACGGTGATGGCGGGCACCGCGCCTGCAGACG
ACGACGACACGGCGGCGGCGGCGGCGGCCGACGAGTACCATGCCGAGGCCATGGATGCCAAGGCCACGTTACAAGACGAG
AGGAAGACTCTCCCGGTGTACAAGCTCAAGGACGACCTGCTCAAGGCCATCGACGAGCACCAGGTCCTGATCGTCGTCGG
CGAGACCGGCTCCGGCAAGACGACGCAGATACCGCAGTACCTCCACGAGGTCGGGTACACGGCGGGGGGGAGGAAGAAGG
TGGCGTGCACGCAGCCGCGGCGCGTGGCGGCGATGAGCGTGGCGGCGAGGGTGGCGGAGGAGATGGGCGTCAAGCTCGGG
CACGAGGTCGGCTACTCCATCCGGTTCGAGGACTGCACGTCGGAGAAGACGGTGATCAAGTACATGACCGACGGGATGCT
CCTCCGCGAGTTCCTCGGCGAGCCCGACCTGGGCAGCTACAGCGTCGTCGTCGTCGACGAGGCCCACGAGCGGACGCTCG
CCACCGACATCCTCTTCGGCCTCGTCAAGGACATCGCCCGCCTCCGCCCTGACATGAAGCTGCTCATCTCCAGCGCGACG
CTCAACGCCGACAAGTTCAGCGACTTCTTCGACGCGGCGCCCGTCTTCCGGATCCCCGGGCGGCGGTTCGAGGTGGGCAT
CCACTACACCGTGGCGCCGGAGGCGGACTACATCGACGCCGCCGTCGTGACGGTGCTGCAGCTGCACGTCACGGAGCCCC
CCGGCGGCGGCGACATCCTGCTGTTCCTCACGGGGCAGGAGGAGATCGAGACGGTGGAGGAGATCCTGAGGCATCGGCTG
CGGGTGCTCGGCGGCAAGGTGGCGGAGCTGGTGATCTGCCCCATCTACGCCAACCTCCCCGCCGAGCTGCAGGCCAAGAT
CTTCGAGCCGGCGCCGGCGGGCGCGCGCAAGGTGGTGCTCGCCACCAACATCGCCGAGACGTCGCTGACCATCGACGGGA
TCAAGTACGTGGTCGACCCGGGGTTCTGCAAGGTGAAGTCGTACAACCCGCGCACCGGGATGGAGTCGCTGGTGGTGGCG
CCGGTGTCGAGGGCGTCGGCGGAGCAGCGCGCCGGCCGGTCGGGGCGCACCGGGCCTGGCGAGTGCTTCCGGCTCTACAC
GGAGTACACCTTCGTCAGCGACCTCGACGACGACGCGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNGCGTGTGTGCGTAAAACGATGGAGGAAAGTTGGGAACCATGGGTATAGAATGCAGCCTTAG

Alignment

ORF - retro_oind_65 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.22 %
• Parental protein coverage: 59.08 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DSGRNVKRRTEEVDDEDDGNDTDEEQERIRDQQERAQLEKNMRERDAANTRKLMERQLSKEEQEEITRRS
          D.GRN..RR....D.E.DG.D..EE.E..RDQ.ERAQLE.N.RERDAA.TR.L..R...K.EQ.E..RRS
Retrocopy DAGRNARRRRSPDDEEEDG-DAGEEEEMERDQIERAQLERNIRERDAASTRRLTDRKTTKREQGELARRS

Parental  QAMDKNDTSDLRKFSRQAYLQKRRDKKIDEIRDEILDHEYIFQDVKLTEAEEKEFRYKKKIYDLVKEHVE
          .AMDKNDTS.LR..SR.AYLQ.R..KK..E.RDEI.DHE..F..V.LT.AEE...R.KK..Y.L....V.
Retrocopy DAMDKNDTSGLRRLSRRAYLQRRKEKKVEEMRDEIVDHEFLFPGVQLTAAEERDMRHKKQVYGL----VH

Parental  SADDVAEYKMPEAYDMGDSVNQEKRFSVAMQRYKDPE--ARD--KMNPFAEQEAWEEHQIGKSKLQFGSK
          ..DD...Y.MP.AYD....V.QEKRFSVA..RY..P...ARD....N...EQEAWEE.QI.KS.LQFGS.
Retrocopy DRDDY--YRMPDAYDAAANVDQEKRFSVARRRYEEPAEAARDGKTANALSEQEAWEEQQIRKSRLQFGSM

Parental  DRKRSSDDYQYVFEDGIDFVKSSVIEGTQHEEDSDQEDIDEKDMLKRELQHVSLN-QDERKTLPIYKFRD
          DR.R..D.Y...F.DG..FV.S.V..GT....D.D.......D....E........QDERKTLP.YK..D
Retrocopy DRGRRGDEYELLFDDGVEFVRSTVMAGTAPADDDDTAAAAAADEYHAEAMDAKATLQDERKTLPVYKLKD

Parental  ELLKAVEEYQVIVIVGETGSGKTTQIPQYLHEAGYTAKG--KVACTQPRRVAAMSVAARVSQEMGVKLGH
          .LLKA..E.QV...VGETGSGKTTQIPQYLHE.GYTA.G..KVACTQPRRVAAMSVAARV..EMGVKLGH
Retrocopy DLLKAIDEHQVLIVVGETGSGKTTQIPQYLHEVGYTAGGRKKVACTQPRRVAAMSVAARVAEEMGVKLGH

Parental  EVGYSIRFEDCTSEKTLIKYMTDGMLLREFLGEPDLASYSVVMVDEAHERTLSTDILFGLVKDISRFRPD
          EVGYSIRFEDCTSEKT.IKYMTDGMLLREFLGEPDL.SYSVV.VDEAHERTL.TDILFGLVKDI.R.RPD
Retrocopy EVGYSIRFEDCTSEKTVIKYMTDGMLLREFLGEPDLGSYSVVVVDEAHERTLATDILFGLVKDIARLRPD

Parental  LKLLISSATLDAEKFSDYFDSAPIFKIPGRRYPVEVHYTKAPEADYIDAAIVTVLQIHVTQPP--GDILV
          .KLLISSATL.A.KFSD.FD.AP.F.IPGRR..V..HYT.APEADYIDAA.VTVLQ.HVT.PP..GDIL.
Retrocopy MKLLISSATLNADKFSDFFDAAPVFRIPGRRFEVGIHYTVAPEADYIDAAVVTVLQLHVTEPPGGGDILL

Parental  FLTGQEEIETIDEILKHRTRGLGTKIAELLICPIYANLPTELQAKIFEPTPEGARKVVLATNIAETSLTI
          FLTGQEEIET..EIL.HR.R.LG.K.AEL.ICPIYANLP.ELQAKIFEP.P.GARKVVLATNIAETSLTI
Retrocopy FLTGQEEIETVEEILRHRLRVLGGKVAELVICPIYANLPAELQAKIFEPAPAGARKVVLATNIAETSLTI

Parental  DGIKYVVDPGFCKIKSYNPRTGMESLLINPISKASANQRAGRSGRTGPGKCFRLYTSYNYMHDLEDN
          DGIKYVVDPGFCK.KSYNPRTGMESL...P.S.ASA.QRAGRSGRTGPG.CFRLYT.Y....DL.D.
Retrocopy DGIKYVVDPGFCKVKSYNPRTGMESLVVAPVSRASAEQRAGRSGRTGPGECFRLYTEYTFVSDLDDD

Legend:

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

Expression

RNA-Seq

Oryza sativa indica was not studied using RNA-Seq expression data.

ChIP-Seq

Oryza sativa indica was not studied using ChIP-Seq data.

EST

Oryza sativa indica was not studied using EST data.

TSS

Oryza sativa indica was not studied using FANTOM5 data.

Lab

retro_oind_65 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza sativa indica 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 16 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA027162	1 retrocopy	retro_oind_65 ,
Brassica oleracea	Bo5g087070	1 retrocopy	retro_bole_7,
Brassica rapa	Bra010168	1 retrocopy	retro_brap_26,
Brachypodium distachyon	BRADI1G61220	1 retrocopy	retro_bdis_4,
Glycine max	GLYMA06G21821	1 retrocopy	retro_gmax_7,
Leersia perrieri	LPERR08G09260	1 retrocopy	retro_lper_14,
Hordeum vulgare	MLOC_5589	1 retrocopy	retro_hvul_14,
Oryza meridionalis	OMERI08G09070	1 retrocopy	retro_omer_5,
Oryza nivara	ONIVA08G11780	1 retrocopy	retro_oniv_26,
Oryza punctata	OPUNC08G10350	1 retrocopy	retro_opun_23,
Oryza glaberrima	ORGLA08G0098600	1 retrocopy	retro_ogla_26,
Oryza rufipogon	ORUFI08G12410	1 retrocopy	retro_oruf_44,
Solanum tuberosum	PGSC0003DMG402024649	1 retrocopy	retro_stub_33,
Prunus persica	PRUPE_ppa000714mg	1 retrocopy	retro_pper_32,
Sorghum bicolor	Sb04g022460	1 retrocopy	retro_sbic_37,
Setaria italica	Si021302m.g	1 retrocopy	retro_sita_41,