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


Retrocopy-Parental alignment summary:






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

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:

ParentalILTALEVLDNSIRLVLEVAQHLGEKMVRTIAMDGTEGLVRGQRVLNTGSPIKVPVGRATLGRIINVIGEP
I.......D..I....EV.Q.LG...VR..AM..T.GL.RG..V..TG.P..VPVG.ATLGRI.NV.GEP
RetrocopyIVKGRDTVDQQINVTCEVQQLLGNNRVRAVAMSATDGLMRGMDVIDTGAPLSVPVGGATLGRIFNVLGEP
ParentalIDERGEIKTDHYLPIHREAPSFVEQATEQEILVTGIKVVDLLAPYQRGGKIGLFGGAGVGKTVLIMELIN
ID..G...T....PIHR.AP.F....T...I..TGIKVVDLLAPY.RGGKIGLFGGAGVGKTVLIMELIN
RetrocopyIDNLGPVDTRTTSPIHRSAPAFIQLDTKLSIFETGIKVVDLLAPYRRGGKIGLFGGAGVGKTVLIMELIN
ParentalNVAKAHGGFSVFAGVGERTREGNDLYREMIESGVIKLGEKQAESKCALVYGQMNEPPGARARVGLTGLTV
N.AKAHGG.SVF.GVGERTREGNDLY.EM.ESGVI......AESK.ALVYGQMNEPPGAR.RVGLT.LT.
RetrocopyNIAKAHGGVSVFGGVGERTREGNDLYMEMKESGVIN-EQNIAESKVALVYGQMNEPPGARMRVGLTALTM
ParentalAEHFRDAEGQDVLLFIDNIFRFTQANSEVSALLGRIPSAVGYQPTLATDLGGLQERITTTKKGSITSVQA
AE.FRD...QDVLLFIDNIFRF.QA.SEVSALLGR.PSAVGYQPTL.T..G.LQERIT.TK.GSITS.QA
RetrocopyAEYFRDVNEQDVLLFIDNIFRFVQAGSEVSALLGRMPSAVGYQPTLSTEMGSLQERITSTKEGSITSIQA
ParentalIYVPADDLTDPAPATTFAHLDATTVLSRQISELGIYPAVDPLDSTSRMLSPHILGQDHYNTARGVQKVLQ
.YVPADDLTDPAPATTFAHLDATTVLSR.....GIYPAVDPLDSTS.ML.P.I.G..HY.TA..V...LQ
RetrocopyVYVPADDLTDPAPATTFAHLDATTVLSRGLAAKGIYPAVDPLDSTSTMLQPRIVGEEHYETAQRVKQTLQ
ParentalNYKNLQDIIAILGMDELSEDDKLTVARARKIQRFLSQPFHVAEVFTGAPGKYVELKESIVSFQGVLDGKY
.YK.LQDIIAILG.DELSE.D.LTVARARKI.RFLSQPF.VAEVFTG.PGKYV.L.E.I..F...L.G..
RetrocopyRYKELQDIIAILGLDELSEEDRLTVARARKIERFLSQPFFVAEVFTGSPGKYVGLAETIKGFKLILSGEL
ParentalDDLPEQSFYMVGGIEEVIAKAEKIAKES
D.LPEQ.FY.VG.I.E..AKA.....E.
RetrocopyDGLPEQAFYLVGNIDEATAKATNLEMEN

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






Amborella trichopoda was not studied using RNA-Seq expression data.
Amborella trichopoda was not studied using ChIP-Seq data.
Amborella trichopoda was not studied using EST data.
Amborella trichopoda was not studied using FANTOM5 data.
retro_atri_7 was not experimentally validated.

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.

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 AT5G086701 retrocopy
Oryza sativa indicaBGIOSGA0176022 retrocopies
Brassica rapa Bra0060132 retrocopies
Chlamydomonas reinhardtii CHLREDRAFT_783481 retrocopy
Aegilops tauschii F775_329461 retrocopy
Hordeum vulgare MLOC_707911 retrocopy
Oryza glaberrima ORGLA01G02201001 retrocopy
Triticum aestivum TRAES3BF058700080CFD_g2 retrocopies



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