RetrogeneDB ID:

retro_atha_14

Retrocopy
location
Organism:Mouse-ear cress (Arabidopsis thaliana)
Coordinates:5:21167431..21169462(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:AT5G52090
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:AT5G37150
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_atha_14
ATGACTTTAACAACAAACACTCGAATTTGGAATGCTTTGCACAACGAAGCTGACATATCGACTCTAACCAAGAGTGTGCT
TCAGGCTAATACTGAGGGTACAGAACAATGTTTTTGTTCTGAAAATGATGGGAGATCTGACCTTGTTTTGGATATAATCC
GTTCAACGAAATTGAACTCTTCCCAAGAGGATGCAATCTTGGGCTGCCTTGAGACAAGAAACTGTACCCATAAGAACAGT
GTGAAACTGATATGGGGACCTCCTAGAACAGGCAAAACAAAGACGGTCGCGACTCTTCTCTTTGCCCTTCTCAAACTAAG
GTGCAAGACAGTTGTGTGTGCTCCTACAAACACAGCTATTGTACAAGTTACATCAAGGCTCTTATCCTTATTTAAGGAAA
ACTCGACAGCGGAAAATGCTACTTACAGGCTAGGGAATATCATTTTATCCGGAAACCGGGACAGAATGGGGATTAACAAG
AACGATCATGTTCTTCTCGATGTGTTTCTTGATGAGCGTATTGGTAAGCTTGGTAAACTGTTTTCACCATTTTCTGGATG
GATGCAGAGATTAGAGTCACTGATACAGTTTCTTGAAAACCCCGAGGGAAAGTATGAGAGACATGTCTACGAGTTAGAAG
AAGTTGAAAGAATGAATGAAGAAGATGAAAGGGAAGAAGTTGTTGTTAACATTCCTACTTTTGGAGAATTCGTTCAGAAG
AATTTTAATAGCTTAAGTGAAGAAGTGAAGACATGCATCGTTGATTTGTATACACATCTTCCCAAGGTTTACCTTCCATA
TGAAGATGTGAAGAAAATGATTGCTTCTCGTCAAACTCTTCAGCGTATCAGATATTTCTTGAGGGAGAATTCTTCTAGGG
TTGATTTCGAGGAAGGAAATTTCAGATTTGATTGCTTCAAAAGACTCAGTGATGATTGCCTCAAGGCTCTACGCTTACTT
CCAAAACGTTTTGAGATTCCAGACATGTTAGAAAACGAAGATATTAGGAAATTTTGTCTTCAAAACGCGGATATTATCCT
CTGCACAGCCTCGGGTGCTGCGGAAATGAACGTGGAAAGGACAGGAAATGTAGAACTGCTTGTGGTTGATGAGGCGGCTC
AGCTTAAGGAATGTGAATCAGTTGCTGCATTGCAACTTCCGGGACTGCGTCACGCCATTTTAATAGGAGATGAGTTTCAA
TTGCCTGCAATGGTTCATAATGAGATGTGTGAAAAGGCGAAATTCGGAAGAAGCTTGTTTGAGAGATTGGTTTTGCTTGG
TCACAACAAACACTTGCTTGATGTTCAATATCGAATGCATCCTTCTATTAGTCGTTTCCCCAACAAGGAGTTTTATGGTG
GGAGAATCAAAGATGCTGAAAATGTTAAAGAAAGTATTTATCAAAAGAGGTTTCTTAAAGGAAACATGTTTGACTCATTT
TCTTTTATCAATGTTGGACGTGGAAAAGAAGAGTTTGGTGATGGACATAGTCCCAAAAACATGGTTGAAGTTGCTGTCAT
TTCTGAAATTATATCAAATCTTTACAAAGTTTCATGTGAAAGGAGGATGAAGGTGAGTGTCGGAGTGGTCTCACCTTACA
AAGGACAGATGAGAGCAATCCAAGAGAAAATCGGAGATAAGTACAGTTCCTTATCAGGTCAGCAATTCACTTTGAATGTT
CGGTCCGTAGATGGTTTTCAAGGAGGAGAAGAAGACATTATCATCATCTCCACCGTTAGAAGTAACGGTAATGGAAAAGT
CGGATTTCTTAACAACCGTCAAAGAGCTAACGTGGCACTGACTCGAGCAAGACACTGTTTATGGGTGATTGGGAACGAGA
CAACTTTGGCTCTAAGTGGTTCGATTTGGGCAACACTGATAAGTGAGTCTAGGACACGTGGATGTTTCCATGATGCTACT
GATGAGATGAATCTAAGAGATGCCATGAATGAAGCTTTGCTTGAGGATGTGTCTTCGAGTCTTGGATCTCTTTCGCTTAG
GAATGGCCATGGAAGAAGAAATGTTTGGTAG

ORF - retro_atha_14 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 94.08 %
Parental protein coverage: 80.33 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMTLTTNTRIWNALHNEAAISTLTKSVLQANT--VNNVFVLKMMGDLTLFLDIIRSTKLNSSQEDAILGCL
MTLTTNTRIWNALHNEA.ISTLTKSVLQANT......F.....G...L.LDIIRSTKLNSSQEDAILGCL
RetrocopyMTLTTNTRIWNALHNEADISTLTKSVLQANTEGTEQCFCSENDGRSDLVLDIIRSTKLNSSQEDAILGCL
ParentalETRNCTHKNSVKLIWGPPGTGKTKTVATLLFALLKLRCKTVVCAPTNTAIVQVASRLLSLFKENSTSENA
ETRNCTHKNSVKLIWGPP.TGKTKTVATLLFALLKLRCKTVVCAPTNTAIVQV.SRLLSLFKENST.ENA
RetrocopyETRNCTHKNSVKLIWGPPRTGKTKTVATLLFALLKLRCKTVVCAPTNTAIVQVTSRLLSLFKENSTAENA
ParentalTYRLGNIILSGNRDRMGIHKNDHVLLDVFLDERIGKLGKLFSPFSGWMQRLESLIQFLENPEGKYERHVY
TYRLGNIILSGNRDRMGI.KNDHVLLDVFLDERIGKLGKLFSPFSGWMQRLESLIQFLENPEGKYERHVY
RetrocopyTYRLGNIILSGNRDRMGINKNDHVLLDVFLDERIGKLGKLFSPFSGWMQRLESLIQFLENPEGKYERHVY
ParentalELEEVERMEEEAERQEVVVNIPTIGEFVKKNFNSLSEEVETCIVDLFTHLPKVYLPYDDVKIMIASRQSL
ELEEVERM.EE.ER.EVVVNIPT.GEFV.KNFNSLSEEV.TCIVDL.THLPKVYLPY.DVK.MIASRQ.L
RetrocopyELEEVERMNEEDEREEVVVNIPTFGEFVQKNFNSLSEEVKTCIVDLYTHLPKVYLPYEDVKKMIASRQTL
ParentalQRIRYFLRENSSRVDFEEGNFRFDCFKRLSVDCLKALRLLPKRFEIPDMLENEDIRKFCLQNADIILCTA
QRIRYFLRENSSRVDFEEGNFRFDCFKRLS.DCLKALRLLPKRFEIPDMLENEDIRKFCLQNADIILCTA
RetrocopyQRIRYFLRENSSRVDFEEGNFRFDCFKRLSDDCLKALRLLPKRFEIPDMLENEDIRKFCLQNADIILCTA
ParentalSGAAEMNVERTGNVELLVVDEAAQLKECESVAALQLPGLRHAILIGDEFQLPAMVHNEMCEKAKFGRSLF
SGAAEMNVERTGNVELLVVDEAAQLKECESVAALQLPGLRHAILIGDEFQLPAMVHNEMCEKAKFGRSLF
RetrocopySGAAEMNVERTGNVELLVVDEAAQLKECESVAALQLPGLRHAILIGDEFQLPAMVHNEMCEKAKFGRSLF
ParentalERLVLLGHNKHLLDVQYRMHPSISRFPNKEFYGGRIKDAENVKESIYQKRFLQGNMFGSFSFINVGRGKE
ERLVLLGHNKHLLDVQYRMHPSISRFPNKEFYGGRIKDAENVKESIYQKRFL.GNMF.SFSFINVGRGKE
RetrocopyERLVLLGHNKHLLDVQYRMHPSISRFPNKEFYGGRIKDAENVKESIYQKRFLKGNMFDSFSFINVGRGKE
ParentalEFGDGHSPKNMVEVAVVSEIISNLFKVSCERRMKVSVGVVSPYKGQMRAIQEKIGDKYSSLSGQQFALNV
EFGDGHSPKNMVEVAV.SEIISNL.KVSCERRMKVSVGVVSPYKGQMRAIQEKIGDKYSSLSGQQF.LNV
RetrocopyEFGDGHSPKNMVEVAVISEIISNLYKVSCERRMKVSVGVVSPYKGQMRAIQEKIGDKYSSLSGQQFTLNV
ParentalRSVDGFQGGEEDIIIISTVRSNSNGKVGFLNNRQRANVALTRARHCLWVIGNETTLALSGSIWATLISES
RSVDGFQGGEEDIIIISTVRSN.NGKVGFLNNRQRANVALTRARHCLWVIGNETTLALSGSIWATLISES
RetrocopyRSVDGFQGGEEDIIIISTVRSNGNGKVGFLNNRQRANVALTRARHCLWVIGNETTLALSGSIWATLISES
ParentalRTRGCFYDATDEMNLRNAMNEALLEDVSSSLGSLSIRNGHGRRNVW
RTRGCF.DATDEMNLR.AMNEALLEDVSSSLGSLS.RNGHGRRNVW
RetrocopyRTRGCFHDATDEMNLRDAMNEALLEDVSSSLGSLSLRNGHGRRNVW

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






RNA-Seq - click to see more details

Arabidopsis thaliana was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Arabidopsis thaliana was not studied using ChIP-Seq data.

EST - click to see more details

Arabidopsis thaliana was not studied using EST data.

TSS - click to see more details

Arabidopsis thaliana was not studied using FANTOM5 data.

Lab - click to see more details

retro_atha_14 was not experimentally validated.

Retrocopy orthology:
Arabidopsis thaliana 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
Arabidopsis thaliana AT5G37150 1 retrocopy
retro_atha_14 ,


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