RetrogeneDB ID:

retro_acar_65

Retrocopy
location
Organism:Anole lizard (Anolis carolinensis)
Coordinates:1:55724266..55725019(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSACAG00000008637
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_acar_65
CTGGTTTGTGATGGAATTGAAAGAGGAACTCACGTCTGGCTTCTAGTCTTCATGCCATTGTTCTTCGTATCTCCAGTGTC
AGTTGGAGCTTGTGTGTGGGGCTTTCACCATGACAGATCTCTGGAGCTGGAAATCCTGTGTTCCGTCAATATTCTCCAGT
TCATATTCATTGCACTCTGTCTGGATGAAATTATCAAGTGGCCATGGCTTGTTGTCTGTGTCCCTTTGTGGATCCTCATG
TCTTTTTTGTGTTTGGTTGTACTCTACTACATCGTCTGGTCTGTCCTGTTCCTGCGTTCCATGAATGTAATTGCTGAACA
AAGGAGAACACACATAACAATGGCTATCAGTTGGATGACAATCGTGGTCCCATTGCTCACCTTTGAAATCCTGCTTGTGC
ACAGACTGGATGTACATAACACATTCTCCTATATATCTATATTTGTCCCTCTTTGGCTTTCAATGATAACCTTAATGGCA
ACAACATTTAGACAGAAGGGAGGCAATCATTGGTGGTTTGGAATTTGCAAGGACTTCTGTCAATTCCTGCTTGAAATTTT
CCCCTTCGTGAGATAGTATGGCAACATTTCCTGTGATCTTCATCATGAAGACAATGATGAGGTGAAAGAAACGCCCATCC
CCGAACCTCCCAAAATTGCTCCAATGTTTTGAAAAAAGACTGGTGTGGTTATTACCCAGAGTCCCGGGAAATACGTCATT
CCGCCTCCCAAACTAAACATTGATATGCTAGAT

ORF - retro_acar_65 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.83 %
Parental protein coverage: 89.64 %
Number of stop codons detected: 2
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalLVCDGIERGTRFWLLVFMPLFFVSPVSVAACVWGFRHDRSLELEILCSVNILQFIFIALRLDEIIKWPWL
LVCDGIERGT..WLLVFMPLFFVSPVSV.ACVWGF.HDRSLELEILCSVNILQFIFIAL.LDEIIKWPWL
RetrocopyLVCDGIERGTHVWLLVFMPLFFVSPVSVGACVWGFHHDRSLELEILCSVNILQFIFIALCLDEIIKWPWL
ParentalVVCVPLWILMSFLCLVVLYYIVWSVLFLRSMDVIAEQRRTHITMAISWMTIVVPLLTFEILLVHRLDGHN
VVCVPLWILMSFLCLVVLYYIVWSVLFLRSM.VIAEQRRTHITMAISWMTIVVPLLTFEILLVHRLD.HN
RetrocopyVVCVPLWILMSFLCLVVLYYIVWSVLFLRSMNVIAEQRRTHITMAISWMTIVVPLLTFEILLVHRLDVHN
ParentalTFSYIPIFVPLWLSLITLMATTFGQKGGNHWWFGIRKDFCQFLLEIFPFLREYGNISYDLHHEDNDEAEE
TFSYI.IFVPLWLS.ITLMATTF.QKGGNHWWFGI.KDFCQFLLEIFPF.R.YGNIS.DLHHEDNDE..E
RetrocopyTFSYISIFVPLWLSMITLMATTFRQKGGNHWWFGICKDFCQFLLEIFPFVR*YGNISCDLHHEDNDEVKE
ParentalTPIPEPPKIAPMFRKKTGVVITQSPGKYVIPPPKLNIDMPD
TPIPEPPKIAPMF.KKTGVVITQSPGKYVIPPPKLNIDM.D
RetrocopyTPIPEPPKIAPMF*KKTGVVITQSPGKYVIPPPKLNIDMLD

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 .00 RPM 14 .70 RPM
SRP009831_brain 0 .05 RPM 40 .14 RPM
SRP009831_dewlap 0 .00 RPM 42 .86 RPM
SRP009831_embryo 0 .15 RPM 23 .00 RPM
SRP009831_heart 0 .00 RPM 22 .93 RPM
SRP009831_liver 0 .00 RPM 9 .33 RPM
SRP009831_lung 0 .05 RPM 20 .20 RPM
SRP009831_ovary 0 .12 RPM 52 .70 RPM
SRP009831_skeletal_muscle 0 .00 RPM 6 .08 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_65 retrocopy.

TSS - click to see more details

Anolis carolinensis was not studied using FANTOM5 data.

Lab - click to see more details

retro_acar_65 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 26 parental genes, and 26 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG00000008637 1 retrocopy
retro_acar_65 ,
Ailuropoda melanoleuca ENSAMEG000000093511 retrocopy
retro_amel_8,
Bos taurus ENSBTAG000000068181 retrocopy
retro_btau_1,
Canis familiaris ENSCAFG000000191031 retrocopy
retro_cfam_159,
Cavia porcellus ENSCPOG000000036221 retrocopy
retro_cpor_5,
Dasypus novemcinctus ENSDNOG000000118641 retrocopy
retro_dnov_2451,
Dipodomys ordii ENSDORG000000150271 retrocopy
retro_dord_67,
Equus caballus ENSECAG000000093991 retrocopy
retro_ecab_426,
Felis catus ENSFCAG000000244831 retrocopy
retro_fcat_1116,
Homo sapiens ENSG000001559841 retrocopy
retro_hsap_104,
Gorilla gorilla ENSGGOG000000242681 retrocopy
retro_ggor_189,
Loxodonta africana ENSLAFG000000030441 retrocopy
retro_lafr_898,
Microcebus murinus ENSMICG000000046391 retrocopy
retro_mmur_106,
Myotis lucifugus ENSMLUG000000013191 retrocopy
retro_mluc_2075,
Macaca mulatta ENSMMUG000000028881 retrocopy
retro_mmul_310,
Mustela putorius furoENSMPUG000000118961 retrocopy
retro_mputfur_46,
Mus musculus ENSMUSG000000731391 retrocopy
retro_mmus_358,
Nomascus leucogenys ENSNLEG000000134871 retrocopy
retro_nleu_2723,
Otolemur garnettii ENSOGAG000000164141 retrocopy
retro_ogar_88,
Procavia capensis ENSPCAG000000091601 retrocopy
retro_pcap_260,
Pongo abelii ENSPPYG000000208091 retrocopy
retro_pabe_118,
Pteropus vampyrus ENSPVAG000000138221 retrocopy
retro_pvam_30,
Rattus norvegicus ENSRNOG000000110471 retrocopy
retro_rnor_6,
Sus scrofa ENSSSCG000000127391 retrocopy
retro_sscr_494,
Ictidomys tridecemlineatus ENSSTOG000000144841 retrocopy
retro_itri_8,
Tursiops truncatus ENSTTRG000000006431 retrocopy
retro_ttru_868,


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