RetrogeneDB ID: retro_oind_60

Retrocopy location

• Organism: Rice subsp. indica (Oryza sativa indica)
• Coordinates: AAAA02042301.1:1522..3046(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BGIOSGA039314
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BGIOSGA025301
• Aliases: None
• Description: None

Sequence

>retro_oind_60
ATGAATGCCCCCCAATCCACGGCCGTCCTGGCGCCGACGGTCAAGCTGCTGATCGGCGGCCAGTTCGTCGAATCGAAGAC
CACCCAGTGGCGCAACGTGGTGAACCCTGCCACGCAGGAAGTGCTGGCGCGCGTGCCCTTCGCCACGCCGGAAGAGATCG
ATGCCGCCGTGGCCTCCGGCAAGGAAGCCTTCAAGAGCTGGAAGAAGACCGCCATCGGCGCCCGGGCGCGCATCTTCCTG
AAATACCAGCAGCTCATCCGCGAGAACATGGCCGAGCTGGCCGCGCTGCTGACGGCCGAGCAGGGCAAGACCCTGCCCGA
TGCAGAAGGCGACGTGTTCCGCGGCCTGGAGGTGGTGGAGCACGCCAGCGCCATCGGCAACCTGCAACTGGGCGAACTGG
CCAACAACGTGGCCGGTGGCGTGGATACCTACACGCTGATGCAGCCGCTGGGCGTGTGCGCGGGCATCACGCCCTTCAAC
TTCCCGGCCATGATCCCGCTCTGGATGTTCCCCATGGCCATCGCCACCGGCAACACCTTCGTGCTCAAGCCCAGCGAGCA
GGACCCGATGGTGACCATGCGCCTGTGCGAACTGGCGCTGGAGGCAGGCATCCCGCCCGGCGTCCTGAACGTGGTGCACG
GCGGCGAGGATGCGGTGAACGCGATCTGCGACCACCAGGACATCAAGGCGATCAGCTTCGTGGGCTCCACCAAGGTCGGC
ACCCATGTGTACAACCGCGCCAGCCTGAATGGCAAGCGCGTGCAGTGCATGATGGGCGCGAAGAACCACGCCATCGTCAT
GCCCGATGCCAACAAGGAGCAGACGCTCAACGCCCTGGCCGGCGCGGCCTTCGGCGCTGCCGGCCAGCGCTGCATGGCAC
TGTCGGTGGTGGTTCTTGTGGGCGAGGCGCAGCAATGGATTTCCGACCTGGTCGCCAAGGCGAAGACGCTCAAGGTCAAT
GCCGGCACCGAGAAAGGCACGGACGTGGGTCCGCTGGTCTCCTGCGCCGCCAGGGACCGCGTCGAAGGACTGATCGAGCG
CGGCATCGCCGACGGCGCCACGCTGGAGCTGGATGGCCGCAAGCCGCAGGTGGCCGGCTTCGAGAAGGGCAACTTCGTCG
GCCCGACCATCTTCAGCGGCGTGAAGCCCGGCATGTCCATCTACGACCAGGAGATCTTCGGCCCCGTGCTATGCCTGGCG
GCGGCCAAGGATATCGAGGAAGCCATCGAATTCATCAACGCCAACCCGAACGGCAACGGCACGGCCATCTTCACCCAGTC
GGGCGCGGCGGCGCGCAAGTTCCAGGAAGAGATCGACGTGGGCCAGGTGGGCATCAACGTGCCGATTCCCGTGCCGGTGC
CCCTCTTCTCGTTCTCGGGCTCGCGCGCCTCCAAGCTCGGCGACCTGGGGCCCTACGGCAAGCAGGTGGTGCTGTTCTAC
ACGCAGACCAAGACGGTGACGGCGCGCTGGTTCGACGACAGCACGATCGGCCATGGCGTGAACACCACCATTAGCCTGAA
GTGA

Alignment

ORF - retro_oind_60 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.29 %
• Parental protein coverage: 89.87 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PRVRLLIGGEFVESRADEHVDVTNPATQEVVSRIPLTTADEFRAAVDAARTAFPGWRNTPVTTRQRIMLK
          P.V.LLIGG.FVES.......V.NPATQEV..R.P..T..E..AAV.....AF..W..T....R.RI.LK
Retrocopy PTVKLLIGGQFVESKTTQWRNVVNPATQEVLARVPFATPEEIDAAVASGKEAFKSWKKTAIGARARIFLK

Parental  YQELIRANMDKLAENITTEQGKTLKDAWGDVFRGLEVVEHACGMGTLQMGEYVSNVSNGIDTFSIREPLG
          YQ.LIR.NM..LA...T.EQGKTL.DA.GDVFRGLEVVEHA...G.LQ.GE...NV..G.DT.....PLG
Retrocopy YQQLIRENMAELAALLTAEQGKTLPDAEGDVFRGLEVVEHASAIGNLQLGELANNVAGGVDTYTLMQPLG

Parental  VCAGICPFNFPAMIPLWMFPIAVTCGNTFVLKPSEKDPGAAMMLAELAMEAGLPKGVLNIVHGTHDVVNN
          VCAGI.PFNFPAMIPLWMFP.A...GNTFVLKPSE.DP...M.L.ELA.EAG.P.GVLN.VHG..D.VN.
Retrocopy VCAGITPFNFPAMIPLWMFPMAIATGNTFVLKPSEQDPMVTMRLCELALEAGIPPGVLNVVHGGEDAVNA

Parental  ICDDEDIKAVSFVGSNIAGMHIYSRASAKGKRVQSNMGAKNHAIILPDADRDATLNALIAAGFGAAGQRC
          ICD..DIKA.SFVGS...G.H.Y.RAS..GKRVQ..MGAKNHAI..PDA....TLNAL..A.FGAAGQRC
Retrocopy ICDHQDIKAISFVGSTKVGTHVYNRASLNGKRVQCMMGAKNHAIVMPDANKEQTLNALAGAAFGAAGQRC

Parental  MALSTAVFVGGSEPWEDELVKRASSLVVNSGMASDADLGPVISKQAKERICKLIQSGADNGARVLLDGRD
          MALS..V.VG....W...LV..A..L.VN.G.....D.GP..S..A..R...LI..G...GA...LDGR.
Retrocopy MALSVVVLVGEAQQWISDLVAKAKTLKVNAGTEKGTDVGPLVSCAARDRVEGLIERGIADGATLELDGRK

Parental  IVVPNFENGNFVGPTLLADVKSEMECYKEEIFGPVLLLMKAESLDDAIQIVNRNKYGNGASIFTTSGVSA
          ..V..FE.GNFVGPT....VK..M..Y..EIFGPVL.L..A.....AI...N.N..GNG..IFT.SG..A
Retrocopy PQVAGFEKGNFVGPTIFSGVKPGMSIYDQEIFGPVLCLAAAKDIEEAIEFINANPNGNGTAIFTQSGAAA

Parental  RKFQTDIEAGQVGINVPIPVPLPFFSFTGSKASFAGDLNFYGKAGVQFFTQIKTVTQQW
          RKFQ..I..GQVGINVPIPVP.P.FSF.GS.AS..GDL..YGK..V.F.TQ.KTVT..W
Retrocopy RKFQEEIDVGQVGINVPIPVPVPLFSFSGSRASKLGDLGPYGKQVVLFYTQTKTVTARW

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_60 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	BGIOSGA025301	1 retrocopy	retro_oind_60 ,