RetrogeneDB ID: retro_oind_103

Retrocopy location

• Organism: Rice subsp. indica (Oryza sativa indica)
• Coordinates: AAAA02048152.1:2..1574(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BGIOSGA021489
• Aliases: None
• Description: None

Sequence

>retro_oind_103
ATGTGTTCTATTTTCGGTGTGCTCGATCTGAAGTCCGATCCCGTTGAACTGCGTAAGAAAGCGCTGGAGCTGTCGCGCCT
GATGCGCCACCGCGGCCCGGATTGGTCCGGCGTTTATGCCAGCGACAAAGCCATTTTGGCCCACGAACGCCTGTCGATCG
TCGACGTCAACAACGGCGCTCAACCGCTGTACAACGCCGCGCACACCCACGTTCTGGCGGTCAACGGCGAAATTTACAAC
CATCAGGCACTGCGCCAACAGCTGAGCGACCGCTATGCCTTCCAGACCGGCTCCGACTGTGAAGTGATCCTGGCGCTGTA
TCAGGAGAAAGGACCGGAGTTCCTCGACGATCTGCAAGGCATGTTCGCCTTTGCCCTGTATGACACCGAAAAAGACGCCT
ACCTGATCGGCCGCGATCACCTGGGCATCATCCCGCTGTACATGGGCCATGACGAACACGGCAACCTGTACGTTGCCTCG
GAAATGAAAGCGCTGGTGCCGGTGTGCCGCACCATCAAGGAATTCCCAGCCGGCAGCTACCTGTGGAGCCAGGACGGCCA
GATCCGCGAATACTATCGCCGCGACTGGTTCGATTACGACAGCGTCAAGGACAACGTGACCGACGCCGCCGCCCTGCGCA
CCGCGCTGGAAGAGTCGGTGAAAAGCCACCTGATGTCCGACGTGCCTTACGGCGTGCTGCTCTCGGGCGGGCTGGATTCT
TCGGTCATTTCGGCGATCACCAAGAAGTACGCCGCACGCCGCGTGGAAGATCAGGAACGCAGCGAAGCCTGGTGGCCGCA
GCTGCACTCCTTCGCCGTCGGGCTGGAAGGCTCGCCGGATCTGCGCGCCGCGCAGGAGGTGGCCAACCATCTGGGCACCG
TGCACCATGAGATCCACTTCACCGTGCAGGAAGGGCTGGACGCCATCCGCGACGTGATTTACCACATCGAAACCTATGAC
GTCACCACCATCCGCGCGTCGACGCCGATGTACCTGATGTCGCGCAAAATCAAGGCGATGGGCATCAAGATGGTGCTTTC
CGGCGAAGGCGCGGACGAAGTGTTCGGCGGCTACCTGTACTTCCATAAGGCGCCGGACGCCCGCGAATTCCACGAAGAGA
CCGTACGCAAACTGCTGGCGCTGCACATGTTCGACTGCGCGCGCGCCAACAAGGCGATGTCCGCCTGGGGCGTCGAAGCC
CGCGTGCCGTTCCTGGACAAGAAATTCCTCGACGTGGCAATGCGCATCAACCCGAAAGATAAAATGTGCGGCAACGGCAA
AATGGAAAAACACATCGTTCGCGAATGTTTCGAGTCCTATTTGCCCGCCAGCGTGGCCTGGCGCCAGAAAGAGCAGTTCT
CCGACGGCGTCGGCTACAGCTGGATCGACACGCTAAAAGAGGTGGCTGCGCAGCAAATTAGCGATCAACAGCTCGAAACC
GCGCGTTTCCGCTTCCCGTACAACACGCCGACGTCGAAAGAAGGCTACCTGTACCGCGAAATCTTCGAGGAGCTGTTCCC
GCTGCCGAGCGCCGCCGAATGCGTGCCGGGCGGCCCATCCGTCGCCTGCTCG

Alignment

ORF - retro_oind_103 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.91 %
• Parental protein coverage: 88.66 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MCGILAVLGVADVSLAKRSRIIELSRRLRHRGPDWSGIHCYQDCYLAHQRLAIVDPTSGDQPLYNEDKSV
          MC.I..VL.........R....ELSR..RHRGPDWSG........LAH.RL.IVD...G.QPLYN.....
Retrocopy MCSIFGVLDLKSDPVELRKKALELSRLMRHRGPDWSGVYASDKAILAHERLSIVDVNNGAQPLYNAAHTH

Parental  VVTVNGEIYNHEELKANLKS-HKFQTASDCEVIAHLYEEYGEEFVDMLDGMFAFVLLDTRDKSFIAARDA
          V..VNGEIYNH..L...L.....FQT.SDCEVI..LY.E.G.EF.D.L.GMFAF.L.DT........RD.
Retrocopy VLAVNGEIYNHQALRQQLSDRYAFQTGSDCEVILALYQEKGPEFLDDLQGMFAFALYDTEKDAYLIGRDH

Parental  IGICPLYMGWGLDGSVWFSSEMKALSDDCERFISFPPGHLYSSKTGGLRRWYNPPWFS-ESIPSTPYNPL
          .GI.PLYMG....G.....SEMKAL...C.....FP.G....S..G..R..Y...WF...S.........
Retrocopy LGIIPLYMGHDEHGNLYVASEMKALVPVCRTIKEFPAGSYLWSQDGQIREYYRRDWFDYDSVKDNVTDAA

Parental  LLRQSFEKAIIKRLMTDVPFGVLLSGGLDSSLVASVV----SRHLAEAKVAAQWGNKLHTFCIGLKGSPD
          .LR...E......LM.DVP.GVLLSGGLDSS...........R..........W...LH.F..GL.GSPD
Retrocopy ALRTALEESVKSHLMSDVPYGVLLSGGLDSSVISAITKKYAARRVEDQERSEAWWPQLHSFAVGLEGSPD

Parental  LRAAKEVADYLGTVHHELHFTVQEGIDALEEVIYHVETYDVTTIRASTPMFLMSRKIKSLGVKMVLSGEG
          LRAA.EVA..LGTVHHE.HFTVQEG.DA...VIYH.ETYDVTTIRASTPM.LMSRKIK..G.KMVLSGEG
Retrocopy LRAAQEVANHLGTVHHEIHFTVQEGLDAIRDVIYHIETYDVTTIRASTPMYLMSRKIKAMGIKMVLSGEG

Parental  SDEIFGGYLYFHKAPNKKEFHEETCRKIKALHLYDCLRANKSTSAWGVEARVPFLDKNFINVAMDIDPEW
          .DE.FGGYLYFHKAP...EFHEET.RK..ALH..DC.RANK..SAWGVEARVPFLDK.F..VAM.I.P..
Retrocopy ADEVFGGYLYFHKAPDAREFHEETVRKLLALHMFDCARANKAMSAWGVEARVPFLDKKFLDVAMRINPKD

Parental  KMIKRDLGRIEKWVLRNAFDDEEKPYLPKHILYRQKEQFSDGVGYSWIDGLKDHANEHVSDSMMMNASFV
          KM.....G..EK...R..F......YLP.....RQKEQFSDGVGYSWID.LK..A....SD.....A.F.
Retrocopy KMCGN--GKMEKHIVRECFES----YLPASVAWRQKEQFSDGVGYSWIDTLKEVAAQQISDQQLETARFR

Parental  YPENTPVTKEAYYYRTIFEKFFPKNAARLTVPGGPSVACS
          .P.NTP..KE.Y.YR.IFE..FP...A...VPGGPSVACS
Retrocopy FPYNTPTSKEGYLYREIFEELFPLPSAAECVPGGPSVACS

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_103 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA021489	1 retrocopy	retro_oind_103 ,