RetrogeneDB ID:

retro_atri_16

Retrocopy
location
Organism:Amborella (Amborella trichopoda)
Coordinates:AmTr_v1.0_scaffold00045:4654416..4657140(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:AMTR_s00045p00224440
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:AMTR_s00035p00184080
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_atri_16
ATGACGTCCCAAATCAGCAGCTCCAATTCTGGATCCAGGTCTTCCTCGCGAGTCCGCGTTGCCAAGGACATTGAAATGAA
TTATGGCCCTGAGGAAGCCAGTCAAATCGCTGGTAACACTTTAATTGTAATTGAGTCCTTGGAAAACAAAGTTGCAGCTG
ATAGAATTATGCAGGTAAAGCGAAAAATTGACGAAAATAAGCAGAAGCTGAAAGGTTTCACTGATCACATTCACAACTTG
TCAAAATCTAGAAAATTGCCTATGGCAAATACGGATTTCTTGATCAAGAGACTAGAAGATGCAACGTGTATGATAAGTGG
CTTAGATTTATCTGCTGGGGAGAGGGAACAGAGTCTTTGTACTGAAGAGTGTCCAAATGCCTCTCCAGCTATTGTTTTTG
GTAGCAATTCCAGTGGAAAAAATGTCGTTCGTCCGATTAAGTTGCCTGAAGAACAGAGAATTCCACCTAACACAGCATGG
CTGTTTTTGGACAGAAATCAAAGAATGACTGAAGACCAATCTGTTTTGGGGCGGAGGCGGATTTACTATGATCGAAGTGG
CGGTGAGGCTCTTATTTGTAGCGACAGTGAAGAAGACCCTGTAGATGATGAAGATGACAAGAAAGAGTTCGGTGATTGTG
AAGATTATATTCTGCAAAAAACCATTGAAGAAGTTGGATTATCCGATACTGTGCTGGATATCCTTGCTCAGCAGTTTCAG
ACAAGTGCTTGTGAAATAAAGGCAAGATATGAATTACTATTAAATCAAGACAAAAGTAAACAATGCACCAGTGAGGAACT
CAATGCGAAACGTGAGCACGCCCTTGCTGGAAAAGATCTGGATGCTGCTCTTGACTCTTTTGATAACCTATTTTGTCGCC
GTTGTCTGGTTTTTGATTGCAGATTGCATGGATGTTCTCAGGACCTAGTTCTTCCGGCTGAGAAGCATCCACCTTGGAGC
AACACCAATGATGATGAACCTTGTTGCACACATTGCTATCGCCTGGCATTAAAACCTGGAACTAATGGTACTGCCAGTGC
ATCTGTGGTCCCTTCATTCTTTGATGCTGATGGTCAGATGTCCTTCCCAAAAAAATCTGGTGGTTCTAGTACTGCTAGGA
GGTTAAAGTCACGGCAGACTGATATTGCTTCTTCCACTGCAAAGCATTTCTTAGCAAGCAGTGGCTCGGAAGCATGCTCT
TCTGCATCTCCTCTAAAAGCTAACCAGGTTGGAAAATATGGAGGGAGGGCTGCTGAGCGAGTTCTCGTTAGCATCCGTAA
GAAACAAAAGAAAATGGTGGTGTCGGACTCAAACACTGGTGTAAGTGGCTCTCTTTGGCCGAGGGATATGAAACTCCGAT
CTAACGCTCGGACGGAAATTTCAGACGCAACATCGTCCACTCAAAGATTATTTTCGAAGTCTGGAAAATCCAGAAAATCT
CGAAAGCAATCTTCCCCAGTCCTTGGTGATGACAATTTGGTGGACGAGAATGTTGATGATGAAGTAAAGGACTCAATGGA
TAAGAAATCAAATATGCATTGCGGACTAGAGATGTCCAGAGATGACAGTTGTGCTAATGCAAATGTCCTTCAATGTGAAG
TAAGCAAGGACAATGCTTGGAAGACCATTGAGAAGTCTTTGTTTGCCACAGGTGTTGAGATCTTTGGTCGGAATAGCTGT
CTCATTGCTAGAAATGTGCTCAATGGCATGAAGACATGTGCTGAAATTGCCCAATACATGAATTTTAACGAAATGAAACC
CTACCTCGGAGCAGGAGAGGGTGCAAATTGTCACAATGATGCATGCGGAATGGCTGATTGTGATGATATCCTGGGGACCA
AACTACGGAGACGATCAAGATTTTTGCGGAGAAGGGGTAGGGCACGTCGGTTGAAGTATACTTGGAAATCTGCGGGTCAT
TCAGCAATTAGGAAAAGAATCACTGATCGGAAGGACCAGCCATGTCGCCAATTCACCCCTTGTAGTTGTCAATCTTCTTG
TGGAAAACAGTGCAGCTGCCTACAACATGGAACATGCTGCGAAAAGTATTGTGGGTGTCCTAAAACTTGCAAGAATCGTT
TTAGGGGATGCCATTGTTCTAAGAGTCAATGCCGAAGTCGGCAATGCCCTTGCTTTGCTGCTGACAGAGAATGTGATCCT
GATGTTTGTAGAAATTGCTGGGCTGGCTGTGGGGATGGGACAATGGGCGGCCCCAGTCAACGAGGTGATAACTACGAGTG
TAGAAATATGAAGCTCCTCCTCAAACAGCAACAGAGGGTGTTACTTGGAAGATCAGATGTTTCTGGCTGGGGTGCTTTCC
TGAAGAATAGTGTGAACAAGCACGAATATATCGGAGAGTACACTGGAGAGTTGATTTCACACCGTGAAGCTGATAAGCGT
GGAAAGATCTATGACCGTGAGAACTCATCCTTCCTTTTCAACTTGAATGATCAGTTTGTCCTTGATGCTTACAGGAAAGG
TGACAAATTAAAATTTGCAAACCACTCCCCAGATCCAAATTGCTATGCCAAGGTTATCATGGTAGCTGGTGATCACAGAG
TAGGTATATTTGCCAAGGAACGGATATGTGCTGGTGAGGAGCTTTTCTATGATTACCGTTATGAGCCGGACTGTGCTCCT
GCATGGGCGAGAGGGCCTGAAGCTTCTAGTTCAAGAAAGGATGAACCGCCTAGTACTCACAGGCGAGCTAAGAAGCTTGC
CTAG

ORF - retro_atri_16 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.59 %
Parental protein coverage: 57.75 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalSSTAKHLLASSSLEAWSRKTNTLLNHSGSPLKAKQVGIYGGTCKRNNKRAAERVLVCIRKKQKKMAVSDS
SSTA..L..S......S......L..SGS...................RAAERVLV.IRKKQKKM.VSDS
RetrocopySSTARRL-KSRQTDIASSTAKHFLASSGSEACSSASPLKANQVGKYGGRAAERVLVSIRKKQKKMVVSDS
ParentalNTGVSGSLWPRDMKLRSNSRKEISDATSSTQRLFSKSPKSRKSRKQSSPIPYDANLVDENVDDEVKDSMD
NTGVSGSLWPRDMKLRSN.R.EISDATSSTQRLFSKS.KSRKSRKQSSP...D.NLVDENVDDEVKDSMD
RetrocopyNTGVSGSLWPRDMKLRSNARTEISDATSSTQRLFSKSGKSRKSRKQSSPVLGDDNLVDENVDDEVKDSMD
ParentalKESKMHSGQEISRDDSCANANVLKCEVSKDNAWKTIEKSLFAKGVEIFGRNSCHIARNVLNGMKTCAEIA
K.S.MH.G.E.SRDDSCANANVL.CEVSKDNAWKTIEKSLFA.GVEIFGRNSC.IARNVLNGMKTCAEIA
RetrocopyKKSNMHCGLEMSRDDSCANANVLQCEVSKDNAWKTIEKSLFATGVEIFGRNSCLIARNVLNGMKTCAEIA
ParentalQYMNFNEMKPYLGAGEGANCHNDACGMADCDDILGTKLRRRSRFLRRRGRVRRLKYTWKSAGHPAIRKRI
QYMNFNEMKPYLGAGEGANCHNDACGMADCDDILGTKLRRRSRFLRRRGR.RRLKYTWKSAGH.AIRKRI
RetrocopyQYMNFNEMKPYLGAGEGANCHNDACGMADCDDILGTKLRRRSRFLRRRGRARRLKYTWKSAGHSAIRKRI
ParentalADRKDQPCRQFTPCSCQSSCGKQCSCLQNGTCCEKYCGCPKTCKNRFRGCHCAKSQCRSRQCPCFAADRE
.DRKDQPCRQFTPCSCQSSCGKQCSCLQ.GTCCEKYCGCPKTCKNRFRGCHC.KSQCRSRQCPCFAADRE
RetrocopyTDRKDQPCRQFTPCSCQSSCGKQCSCLQHGTCCEKYCGCPKTCKNRFRGCHCSKSQCRSRQCPCFAADRE
ParentalCDPDVCRNCWVGCGDGTMGGPNQRGDNYECRNMKLLLKQQQRVLLGRSDVSGWGAFLKNSVNKHEYLGEY
CDPDVCRNCW.GCGDGTMGGP.QRGDNYECRNMKLLLKQQQRVLLGRSDVSGWGAFLKNSVNKHEY.GEY
RetrocopyCDPDVCRNCWAGCGDGTMGGPSQRGDNYECRNMKLLLKQQQRVLLGRSDVSGWGAFLKNSVNKHEYIGEY
ParentalTGELISHREADKRGKIYDRENSSFLFNLNDQFVLDAYRKGDKLKFANHSPDPNCYAKVIMVAGDHRVGIF
TGELISHREADKRGKIYDRENSSFLFNLNDQFVLDAYRKGDKLKFANHSPDPNCYAKVIMVAGDHRVGIF
RetrocopyTGELISHREADKRGKIYDRENSSFLFNLNDQFVLDAYRKGDKLKFANHSPDPNCYAKVIMVAGDHRVGIF
ParentalAKERICAGEELFYDYRYEPDRAPAWARKPEASSSRKDELTSTHGRAKKLA
AKERICAGEELFYDYRYEPD.APAWAR.PEASSSRKDE..STH.RAKKLA
RetrocopyAKERICAGEELFYDYRYEPDCAPAWARGPEASSSRKDEPPSTHRRAKKLA

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






RNA-Seq - click to see more details

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

ChIP-Seq - click to see more details

Amborella trichopoda was not studied using ChIP-Seq data.

EST - click to see more details

Amborella trichopoda was not studied using EST data.

TSS - click to see more details

Amborella trichopoda was not studied using FANTOM5 data.

Lab - click to see more details

retro_atri_16 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 1 parental gene, and 1 retrocopy.

Species Parental gene accession Retrocopies number
Amborella trichopoda AMTR_s00035p00184080 1 retrocopy
retro_atri_16 ,


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