RetrogeneDB ID:

retro_acar_100

Retrocopy
location
Organism:Anole lizard (Anolis carolinensis)
Coordinates:3:156802498..156804194(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSACAG00000002154
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:CROT
Ensembl ID:ENSACAG00000016327
Aliases:None
Description:carnitine O-octanoyltransferase [Source:HGNC Symbol;Acc:2366]


Retrocopy-Parental alignment summary:






>retro_acar_100
ATGGCTGACCATTCTGAAGAGTGCACATTTCAATACCAGAGTTCTCTTCCTTCATTGCCAGTTCCTGCTCTTGATGAATC
ATTACAGAAATACCTCGATTCAGTGAGACCTTTCCTAAAGGAGGAAGAATTTCAGCAAACTCAGGACATAGTAGAAAGAT
TTGAAAATGGAATTGGAAAGGAACTGCATCAAAAATTATTTGAAAGAGCAAAAGTGAAGTGGAATTGGCTTGAGGAATGG
TGGCTCAATGTAGCCTATCTCGAAGCCCACTTATCAACACAAATCTATTATAATTTTGGAGGCCCAGGTCCTTACCTTGA
ACACTTCTGGCCAATGAAAGAAGGGACTCAGATAGAAAGAGGCTCCATAACTATATGGATTTCTTTGAAATTCTGGGAAC
TACTGAGAACAGAAAAGTTGCGTGTCCACAAATCAAATAATATGCCTCTGGATATGAATCAGTTCCGAATGCTGTTTTGC
ACTTGCATGATTCCAGGAACTGTGCAAGATTCAATTGCCAATTATTTCAGGACAGAGAGTGAAGGTGAATGCCCATCTCA
TTTGGTAGTGCTGTGCCGAGGTCGAATTTTTGCATTTGATGGGGTACATGATGGCCATATATTAACCCCACCAGAGATTT
GTAGGCAGCTTTACTACATCCAAGAGATATGTCACAATGAACCTAAGGGACCTGGACTGGCTGCATTAACCTCTGAGTAA
AGAACCCCATGGGCAAAGACACGTGAATATCTTATCAACCTAGATACAAAGAATTTGCTCCATTTGGAAAAAATACAGAA
CAGCTTATTTGTGATCTCCTTAGATGAAGCAAGTCCCCAAGCCACTTCTGAAGATTATTCAGAGGTCACCAAGTTGTCAC
CAACAGGCGATCCAACATTAAGTTCGGGAGACAAATCCTATAACAAGATTATGTTTTTGAATGGATTATTTGGCTCAAAT
TGTGATCACTCTCCTTTTGATGCCATGGTTTTGGTTGTCTTCTGTTCTTTTATTGACTCCAAAATCATCGAATTAGAGGG
AAAATGGAAGGGATCAGAAAGAGTGCGGGATATCCCTTGGCCAGAGGAGCTTTTGTTCAGTTTGGATCAGAAAGTGCTAA
AAGACATTGCTCATGCTAAGGAGCAGTATGAAAAGAAGACACCTGATGTAGAATTGGTGAATTATGCTTTTACTTTCTTT
GACAAAGCTCTGATAAAGAAACAGAAGCTTTATCCTGATATATTCGTTCAGCTTGCTCTTCATGGCTTATTACTGACATC
ATGGACACCCAGGTTGCTGCTATGAAACTGCTACAACCAGACCCTATTACCATGGCCTCATAGAAACTATGCGGCCCTGC
ACCATAGAAGCAGTTGAATGATGTAAATCCATGCTCGATCCAACTTTTAATATCGGCCAACGAAAGCACCTTATGCTGAA
GGCCTTTGCAAAGCACCATAAACGGATGAAAGAGTATGAAATTGGAAAAGGATTTGGCTGTCACCTCTTAGGCCTTCGGT
TTCTCTCCAAAGAGCACAGCCATCCTATGCCTGAAATCTTCCTGAATACTGCTTTCAGTAGAAGTGGAGGAGGTGAAAAC
TTTGTTCTTTCCACTAGCTTGGTAGGCTACACAAGAGTTGGGGGAGCTGTTGTTCCAATAGTATACCATGGTTATGGCTT
TTTCTACAGAATTAGA

ORF - retro_acar_100 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.3 %
Parental protein coverage: 91.44 %
Number of stop codons detected: 3
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalVTDHSEERTFQYQSSLPSLPVPALDESLQKYLDSVRPFLKEEEFQRTQDIVKRFENGIGKELHQKLLERA
..DHSEE.TFQYQSSLPSLPVPALDESLQKYLDSVRPFLKEEEFQ.TQDIV.RFENGIGKELHQKL.ERA
RetrocopyMADHSEECTFQYQSSLPSLPVPALDESLQKYLDSVRPFLKEEEFQQTQDIVERFENGIGKELHQKLFERA
ParentalKVKRNWLEEWWLNVAYLEARLPTQIYYNFGGPGPYLEHFWPMKEGTQIERGSITVWISLKFWELLRTEKL
KVK.NWLEEWWLNVAYLEA.L.TQIYYNFGGPGPYLEHFWPMKEGTQIERGSIT.WISLKFWELLRTEKL
RetrocopyKVKWNWLEEWWLNVAYLEAHLSTQIYYNFGGPGPYLEHFWPMKEGTQIERGSITIWISLKFWELLRTEKL
ParentalRVHKSNNTPLDMNQFRMLFCTCKIPGIVQDSIANYFRTESEGECPSHLVVLCRGRIFAFDGVHDGHILTP
RVHKSNN.PLDMNQFRMLFCTC.IPG.VQDSIANYFRTESEGECPSHLVVLCRGRIFAFDGVHDGHILTP
RetrocopyRVHKSNNMPLDMNQFRMLFCTCMIPGTVQDSIANYFRTESEGECPSHLVVLCRGRIFAFDGVHDGHILTP
ParentalPEICRQLYYIQERCHNEPKGPGLAALTSEERTPWAKTREYLINLDPKNLLHLEKIQSSLFVISLDEASPQ
PEICRQLYYIQE.CHNEPKGPGLAALTSE.RTPWAKTREYLINLD.KNLLHLEKIQ.SLFVISLDEASPQ
RetrocopyPEICRQLYYIQEICHNEPKGPGLAALTSE*RTPWAKTREYLINLDTKNLLHLEKIQNSLFVISLDEASPQ
ParentalATPEDYSEVTKLSLTGDPTLRWGDKSYNKIMFSNGLFGSNCDHSPFDAMVLVVFCSFIDSKIIELEGKWK
AT.EDYSEVTKLS.TGDPTL..GDKSYNKIMF.NGLFGSNCDHSPFDAMVLVVFCSFIDSKIIELEGKWK
RetrocopyATSEDYSEVTKLSPTGDPTLSSGDKSYNKIMFLNGLFGSNCDHSPFDAMVLVVFCSFIDSKIIELEGKWK
ParentalGSERVRDIPWPEELLFSLDQKVLKDVAHAKEQYEKKTSDVELVNYAFTSFGKALIKKQKLHPDIFVQLAL
GSERVRDIPWPEELLFSLDQKVLKD.AHAKEQYEKKT.DVELVNYAFT.F.KALIKKQKL.PDIFVQLAL
RetrocopyGSERVRDIPWPEELLFSLDQKVLKDIAHAKEQYEKKTPDVELVNYAFTFFDKALIKKQKLYPDIFVQLAL
Parental-QLAYYRHHGHPGCCYETATTRRYYHGRTETMRPCTIEALEWCKSMLDPAFTLGQRKHLMLKAFAKHHKL
....Y..H.GHPGCCYETATTR.YYHG..ETMRPCTIEA.E.CKSMLDP.F..GQRKHLMLKAFAKHHK.
Retrocopy>MAYY*HH-GHPGCCYETATTRPYYHGLIETMRPCTIEAVE*CKSMLDPTFNIGQRKHLMLKAFAKHHKR
ParentalMKECENGKGFDRHLLGLLLLSKEHSLPMPEIFLDPAFSRSGGGGNFVLSTSLVGYTRVGGAVVPMVHHGY
MKE.E.GKGF..HLLGL..LSKEHS.PMPEIFL..AFSRSGGG.NFVLSTSLVGYTRVGGAVVP.V.HGY
RetrocopyMKEYEIGKGFGCHLLGLRFLSKEHSHPMPEIFLNTAFSRSGGGENFVLSTSLVGYTRVGGAVVPIVYHGY
ParentalGFFYRIR
GFFYRIR
RetrocopyGFFYRIR

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






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP009831_adrenal 0 .53 RPM 24 .81 RPM
SRP009831_brain 0 .14 RPM 19 .36 RPM
SRP009831_dewlap 0 .38 RPM 78 .47 RPM
SRP009831_embryo 0 .95 RPM 51 .30 RPM
SRP009831_heart 0 .47 RPM 32 .63 RPM
SRP009831_liver 0 .37 RPM 80 .86 RPM
SRP009831_lung 0 .30 RPM 68 .46 RPM
SRP009831_ovary 0 .50 RPM 69 .92 RPM
SRP009831_skeletal_muscle 0 .25 RPM 37 .91 RPM

ChIP-Seq - click to see more details

Anolis carolinensis was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_acar_100 retrocopy.

TSS - click to see more details

Anolis carolinensis was not studied using FANTOM5 data.

Lab - click to see more details

retro_acar_100 was not experimentally validated.

Retrocopy orthology:
Anolis carolinensis 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
Anolis carolinensis ENSACAG00000016327 1 retrocopy
retro_acar_100 ,


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