RetrogeneDB ID:

retro_acar_79

Retrocopy
location
Organism:Anole lizard (Anolis carolinensis)
Coordinates:2:37540517..37542202(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSACAG00000016475
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:TRIM2
Ensembl ID:ENSACAG00000015934
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_acar_79
ATGGATGTCCTGCAGCGAACTCCAGAAAATAGCATTGAGGAGTCTTCCATCCTGGAGACTGTCACAGCTGTTGCTGCAGG
GAAACCACTTTCCTGCCCCAATCATGAAGGAAATTTGATGGAATTTTACTGTCAGTCTTGTGAGACAGCCATGTGCCGGG
AATGTACAGAAGGAGAGCATGCGGAGCATCCCACAGTGCCTCTCAAGGATGTTGTTGAACAACACAAGGGTTCTCTTCAA
GCACAATAGATGCTGTCAATAAAAGACTTCCAGAGATAGATACTGCACTTCATTTCATATCTGAAATTATACATCAGCTG
ACCAACCAAAAGACCAACATCGTTGATGAAATTCATTCCACTTTTGATGAACTCCAGAAAACTTTAAATGTTCGCAAGAG
TGTACTACTTATGGAACTGGAAGTCAATTATGGCCTTAAACATAAAGTTTTGCAGAATCAACTTGATACCCTCTTGGAAG
GACAGGAAAACATTAAGAGTTGTAGCAATTTTACAGCCCAAGCACTCAATCATGGAACAGAAACAGAAGTCTTGCTTGTC
AAGAAGCAAATGAGTGACAAGCTGAACGATCTGGCTGACAGAGATTTCCCACTGCAGCCCCGCGAAAATGATCAGCTGGA
CTTCATAGTGGAAACAGATGGGCTGAAGAAGTCCATTCATAACCTTGGCACTATTTTAACCACAAATGCTGTTGCTTCTG
AAACAGTGGCCACAGGCGAAGGGCTGAAGCAGACGGTGATAGGACAGCCTATGTCAGTCACCATCACTACTAAGGACAAG
GATGGTGAGCTCTGCAAATCTGGGAACGCTTACCTGACTGCTGAGCTGAGTACCCCTGATGGGAGTGTAGCCGATGGAGA
AATACTTGACAACAAAAATGGCACTTACGAATGTCTGTATACTGTCCAGAAAGAAGGGGATTTTACTCTTTCACTGAGAC
TCTATGATCAGCATATTAGGGGCAGCCCATTCAAACTCAAGTTAATCAGATCAGCGGATGTGTCCCCGACCACTGAAGGA
GTTAAAAGGCGTGTGAAGTCTCCTGGTAGTGGCCATGTAAAGCAGAAGGCGGTAAAAAGACCGGCTAGTTTGTACAGCAC
TGGCAAAAGGGAAGAGAACCCCATTGAAGATGATTTGATCTTCAGAGTAGGTACCAAAGGGAGAAACAAAGGAGAGTTTA
CAAATCTTCAGGGAGTAGCTGCATCTACAAATGGAAAAATATTAATAGCAGATAGCAATAATCAGTGTGTACAGGTGTTT
TCCACTGATGGCCAGTTCAAGAGCCGTTTTGGTATTCGGGGAAGGTCTCCCGGTCAGTTGCAGCGGCCTACAGGAGTGGC
TGTGCATCCTTGTGGGGACATCATTATTGCCGACTATGATAATAAATGGGTTAGCATATTCTCCTCTGATGGAAAATTTA
AGACAAAAATTGGGTCTGGAAAACTTATGGGACCAAAAGGTGTTTCTGTGGATCGAAATGGGCACATCATTGTTGTGGAC
AACAAAGCATGTTGTGTGTTCATCTTCCAGCCTAATGGAAAAATAGTAACCAGGTTTGGAAGCCGAGGCAACGGAGACAA
ACAGTTTGCAGGTCCCCATTTTGCAGCTGTCAACCACAATAATGAAATTATTATTACTGATTTCCACAATCATTCTGTCA
AGGTA

ORF - retro_acar_79 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 99.11 %
Parental protein coverage: 85.41 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMDVLQRTPENSIEESSILETVTAVAAGKPLSCPNHEGNLMEFYCQSCETAMCRECTEGEHAEHPTVPLKD
MDVLQRTPENSIEESSILETVTAVAAGKPLSCPNHEGNLMEFYCQSCETAMCRECTEGEHAEHPTVPLKD
RetrocopyMDVLQRTPENSIEESSILETVTAVAAGKPLSCPNHEGNLMEFYCQSCETAMCRECTEGEHAEHPTVPLKD
ParentalVVEQHKGSLQAQ-LDAVNKRLPEIDTALHFISEIIHQLTNQKTNIVDEIHSTFDELQKTLNVRKSVLLME
VVEQHKGSLQAQ..DAVNKRLPEIDTALHFISEIIHQLTNQKTNIVDEIHSTFDELQKTLNVRKSVLLME
RetrocopyVVEQHKGSLQAQ<IDAVNKRLPEIDTALHFISEIIHQLTNQKTNIVDEIHSTFDELQKTLNVRKSVLLME
ParentalLEVNYGLKHKVLQNQLDTLLEGQENIKSCSNFTAQALNHGTETEVLLVKKQMSDKLNDLADRDFPLQPRE
LEVNYGLKHKVLQNQLDTLLEGQENIKSCSNFTAQALNHGTETEVLLVKKQMSDKLNDLADRDFPLQPRE
RetrocopyLEVNYGLKHKVLQNQLDTLLEGQENIKSCSNFTAQALNHGTETEVLLVKKQMSDKLNDLADRDFPLQPRE
ParentalNDQLDFIVETDGLKKSIHNLGTILTTNAVASETVATGEGLKQTVIGQPMSVTITTKDKDGELCKSGNAYL
NDQLDFIVETDGLKKSIHNLGTILTTNAVASETVATGEGLKQTVIGQPMSVTITTKDKDGELCKSGNAYL
RetrocopyNDQLDFIVETDGLKKSIHNLGTILTTNAVASETVATGEGLKQTVIGQPMSVTITTKDKDGELCKSGNAYL
ParentalTAELSTPDGSVADGEILDNKNGTYEFLYTVQKEGDFTLSLRLYDQHIRGSPFKLKLIRSADVSPTTEGVK
TAELSTPDGSVADGEILDNKNGTYE.LYTVQKEGDFTLSLRLYDQHIRGSPFKLKLIRSADVSPTTEGVK
RetrocopyTAELSTPDGSVADGEILDNKNGTYECLYTVQKEGDFTLSLRLYDQHIRGSPFKLKLIRSADVSPTTEGVK
ParentalRRVKSPGSGHVKQKAVKRPASMYSTGKRKENPIEDDLIFRVGTKGRNKGEFTNLQGVAASTNGKILIADS
RRVKSPGSGHVKQKAVKRPAS.YSTGKR.ENPIEDDLIFRVGTKGRNKGEFTNLQGVAASTNGKILIADS
RetrocopyRRVKSPGSGHVKQKAVKRPASLYSTGKREENPIEDDLIFRVGTKGRNKGEFTNLQGVAASTNGKILIADS
ParentalNNQCVQVFSTDGQFKSRFGIRGRSPGQLQRPTGVAVHPCGDIIIADYDNKWVSIFSSDGKFKTKIGSGKL
NNQCVQVFSTDGQFKSRFGIRGRSPGQLQRPTGVAVHPCGDIIIADYDNKWVSIFSSDGKFKTKIGSGKL
RetrocopyNNQCVQVFSTDGQFKSRFGIRGRSPGQLQRPTGVAVHPCGDIIIADYDNKWVSIFSSDGKFKTKIGSGKL
ParentalMGPKGVSVDRNGHIIVVDNKACCVFIFQPNGKIVTRFGSRGNGDKQFAGPHFAAVNHNNEIIITDFHNHS
MGPKGVSVDRNGHIIVVDNKACCVFIFQPNGKIVTRFGSRGNGDKQFAGPHFAAVNHNNEIIITDFHNHS
RetrocopyMGPKGVSVDRNGHIIVVDNKACCVFIFQPNGKIVTRFGSRGNGDKQFAGPHFAAVNHNNEIIITDFHNHS
ParentalVKV
VKV
RetrocopyVKV

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 .07 RPM 0 .79 RPM
SRP009831_brain 0 .19 RPM 99 .37 RPM
SRP009831_dewlap 0 .72 RPM 131 .79 RPM
SRP009831_embryo 0 .12 RPM 25 .84 RPM
SRP009831_heart 0 .10 RPM 15 .77 RPM
SRP009831_liver 0 .00 RPM 3 .97 RPM
SRP009831_lung 0 .10 RPM 18 .08 RPM
SRP009831_ovary 0 .58 RPM 136 .56 RPM
SRP009831_skeletal_muscle 0 .04 RPM 7 .98 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_79 retrocopy.

TSS - click to see more details

Anolis carolinensis was not studied using FANTOM5 data.

Lab - click to see more details

retro_acar_79 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 ENSACAG00000015934 1 retrocopy
retro_acar_79 ,


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