RetrogeneDB ID: retro_atri_7

Retrocopy location

• Organism: Amborella (Amborella trichopoda)
• Coordinates: AmTr_v1.0_scaffold00334:18755..20135(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: AMTR_s00334p00013670
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: AMTR_s00006p00059970
• Aliases: None
• Description: None

Sequence

>retro_atri_7
ATGCCTAATATTTACAATGCTTTGATAGTTAAGGGTCGAGATACTGTTGATCAACAAATTAATGTGACTTGTGAAGTACA
GCAATTATTAGGAAATAATCGAGTTAGAGCTGTAGCTATGAGTGCTACAGATGGTCTAATGAGAGGAATGGATGTGATTG
ACACAGGAGCTCCTTTAAGTGTTCCAGTCGGCGGAGCGACACTAGGACGAATTTTCAACGTACTTGGGGAGCCCATTGAT
AATTTAGGTCCGGTAGATACTCGCACAACATCTCCTATTCATAGATCTGCACCTGCCTTTATACAATTAGATACAAAATT
ATCGATTTTTGAAACAGGAATTAAAGTAGTAGATCTTTTAGCCCCTTATCGCCGTGGAGGAAAAATAGGACTCTTCGGGG
GTGCTGGAGTAGGTAAAACAGTACTCATTATGGAATTGATCAACAACATTGCCAAAGCTCATGGGGGCGTATCCGTATTT
GGCGGAGTAGGTGAACGTACCCGTGAAGGAAATGATCTTTACATGGAAATGAAAGAATCTGGCGTAATTAATGAACAAAA
TATTGCCGAATCAAAAGTGGCTCTAGTCTATGGTCAGATGAATGAACCACCAGGGGCTCGTATGAGAGTTGGTTTAACTG
CTCTAACTATGGCGGAGTATTTCCGAGATGTTAATGAACAAGACGTACTTCTATTTATTGACAATATCTTTCGTTTTGTC
CAAGCAGGATCCGAAGTATCCGCCTTATTAGGCAGAATGCCTTCCGCTGTAGGTTATCAACCCACTCTTAGTACTGAAAT
GGGTTCTTTACAAGAAAGAATTACTTCTACCAAAGAGGGGTCCATAACTTCTATTCAAGCAGTTTATGTACCCGCGGACG
ATTTGACTGATCCAGCTCCGGCCACGACATTTGCACATTTAGATGCGACTACCGTACTATCAAGAGGATTGGCCGCCAAA
GGCATCTATCCAGCAGTAGATCCTTTAGATTCAACGTCAACTATGCTCCAACCTCGGATTGTTGGTGAAGAACATTATGA
AACTGCGCAAAGAGTTAAACAAACTTTACAACGTTACAAAGAACTTCAGGACATTATAGCTATTCTTGGGTTGGACGAAT
TATCCGAAGAAGACCGCTTAACCGTAGCAAGAGCACGAAAAATTGAGCGTTTCTTGTCACAACCTTTTTTCGTAGCAGAA
GTATTTACAGGTTCCCCGGGGAAATATGTTGGTCTAGCAGAAACAATTAAAGGGTTTAAATTGATTCTTTCTGGAGAATT
AGATGGTCTTCCTGAACAGGCTTTTTATTTGGTCGGTAACATTGATGAAGCTACTGCGAAGGCTACGAACTTAGAAATGG
AGAACAAATTGAAGAAATGA

Alignment

ORF - retro_atri_7 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.09 %
• Parental protein coverage: 80. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ILTALEVLDNSIRLVLEVAQHLGEKMVRTIAMDGTEGLVRGQRVLNTGSPIKVPVGRATLGRIINVIGEP
          I.......D..I....EV.Q.LG...VR..AM..T.GL.RG..V..TG.P..VPVG.ATLGRI.NV.GEP
Retrocopy IVKGRDTVDQQINVTCEVQQLLGNNRVRAVAMSATDGLMRGMDVIDTGAPLSVPVGGATLGRIFNVLGEP

Parental  IDERGEIKTDHYLPIHREAPSFVEQATEQEILVTGIKVVDLLAPYQRGGKIGLFGGAGVGKTVLIMELIN
          ID..G...T....PIHR.AP.F....T...I..TGIKVVDLLAPY.RGGKIGLFGGAGVGKTVLIMELIN
Retrocopy IDNLGPVDTRTTSPIHRSAPAFIQLDTKLSIFETGIKVVDLLAPYRRGGKIGLFGGAGVGKTVLIMELIN

Parental  NVAKAHGGFSVFAGVGERTREGNDLYREMIESGVIKLGEKQAESKCALVYGQMNEPPGARARVGLTGLTV
          N.AKAHGG.SVF.GVGERTREGNDLY.EM.ESGVI......AESK.ALVYGQMNEPPGAR.RVGLT.LT.
Retrocopy NIAKAHGGVSVFGGVGERTREGNDLYMEMKESGVIN-EQNIAESKVALVYGQMNEPPGARMRVGLTALTM

Parental  AEHFRDAEGQDVLLFIDNIFRFTQANSEVSALLGRIPSAVGYQPTLATDLGGLQERITTTKKGSITSVQA
          AE.FRD...QDVLLFIDNIFRF.QA.SEVSALLGR.PSAVGYQPTL.T..G.LQERIT.TK.GSITS.QA
Retrocopy AEYFRDVNEQDVLLFIDNIFRFVQAGSEVSALLGRMPSAVGYQPTLSTEMGSLQERITSTKEGSITSIQA

Parental  IYVPADDLTDPAPATTFAHLDATTVLSRQISELGIYPAVDPLDSTSRMLSPHILGQDHYNTARGVQKVLQ
          .YVPADDLTDPAPATTFAHLDATTVLSR.....GIYPAVDPLDSTS.ML.P.I.G..HY.TA..V...LQ
Retrocopy VYVPADDLTDPAPATTFAHLDATTVLSRGLAAKGIYPAVDPLDSTSTMLQPRIVGEEHYETAQRVKQTLQ

Parental  NYKNLQDIIAILGMDELSEDDKLTVARARKIQRFLSQPFHVAEVFTGAPGKYVELKESIVSFQGVLDGKY
          .YK.LQDIIAILG.DELSE.D.LTVARARKI.RFLSQPF.VAEVFTG.PGKYV.L.E.I..F...L.G..
Retrocopy RYKELQDIIAILGLDELSEEDRLTVARARKIERFLSQPFFVAEVFTGSPGKYVGLAETIKGFKLILSGEL

Parental  DDLPEQSFYMVGGIEEVIAKAEKIAKES
          D.LPEQ.FY.VG.I.E..AKA.....E.
Retrocopy DGLPEQAFYLVGNIDEATAKATNLEMEN

Legend:

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

Expression

RNA-Seq

Amborella trichopoda was not studied using RNA-Seq expression data.

ChIP-Seq

Amborella trichopoda was not studied using ChIP-Seq data.

EST

Amborella trichopoda was not studied using EST data.

TSS

Amborella trichopoda was not studied using FANTOM5 data.

Lab

retro_atri_7 was not experimentally validated.

Homology

Retrocopy orthology:

Amborella trichopoda 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 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Amborella trichopoda	AMTR_s00006p00059970	1 retrocopy	retro_atri_7 ,
Arabidopsis thaliana	AT5G08670	1 retrocopy	retro_atha_12,
Oryza sativa indica	BGIOSGA017602	2 retrocopies	retro_oind_104, retro_oind_87,
Brassica rapa	Bra006013	2 retrocopies	retro_brap_51, retro_brap_57,
Chlamydomonas reinhardtii	CHLREDRAFT_78348	1 retrocopy	retro_crei_1,
Aegilops tauschii	F775_32946	1 retrocopy	retro_atau_18,
Hordeum vulgare	MLOC_70791	1 retrocopy	retro_hvul_13,
Oryza glaberrima	ORGLA01G0220100	1 retrocopy	retro_ogla_47,
Triticum aestivum	TRAES3BF058700080CFD_g	2 retrocopies	retro_taes_170, retro_taes_31,