RetrogeneDB ID:

retro_acar_54

Retrocopy
location
Organism:Anole lizard (Anolis carolinensis)
Coordinates:GL343332.1:1361661..1363413(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSACAG00000006511
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:GALNT12
Ensembl ID:ENSACAG00000002302
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_acar_54
ATGAAGGTCCGACTGTCCAGGAAGGGGCCCTACCTGCTGCTGGGGCTCCTGATTGTCGGGGGCACTTTCTTCCTGGTGGA
GCTGTCTATTTCCAGCCTCCAGGCACCTTCCTCGGGGGGCCTGGGGGATGGGGCCACCAAAGGGAGGTGGGAGAGGCATT
TTTTGAAGGGGGCCGAGGAGAGGGAAGAGCTGGCCCGGCCGGTGTACCAGAAGCCCCCTCCGGACCCCCATGGCCTGGGG
GAGTGGGGCAAGGCAGCCCGCTTGACTCTGAGCCCTGAAGAGAAGAAGCTGGAAGAAGAGCTGGTGGAGCGCTACGCCAT
CAACATCTACTTGAGCGATAAGATCTCTCTGCACCGCCACATCGATGATGGGCGCATGCCAGAGTGCAGGTCCAAGACCT
ATGACTACCGGCGGCTGCCCACCACCTCCGTCATCATCGCGTTCTACAACGAAGCCTGGTCCACTTTGCTCCGGACCATC
CACAGCGTTCTGGAGTCCTCACCGTCCGTCCTGCTCAAGGAGATAATTCTGGTGGACGACCTGAGCGACAAAGTGTACCT
GAAGGGCGAGCTCGAAAAGTACATCAGCAACCTGCAAAGGGTCCGCTTGATCAGAACCAACAAGCGGGAAGGGCTGGTCC
GGGCCAGGCTGATCGGTGCCACCTTTGCCACGGGCGACGTCCTCACCTTCCTCGACTGCCATTGTGAGTGTGTCCCTGGG
TGGCTGGAGCCGCTTCTGCAGAGGGTGGCTGAGAACGAGAGCGTCATCATTTGCCCCGTCATCGACACCATTGATTGGAA
CACCTTTGAGTTCTACATGCAGCCGGGAGAGCCCATGATTGGGGGGTTTGACTGGCGGCTGACCTTTCAGTGGCACTCGG
TGCCAGACTACGAGCGCCAACGGCGGAAATCTAAAGTTGACCCCATAAGATCCCCGACCATGGCTGGAGGCCTGTTTGCT
GTCAGTAAAAAGTACTTTGAATATCTTGGCACCTATGACATGGGGATGGATGTGTGGGGCGGAGAGAACCTGGAGCTCTC
CTTTAGGGTCTGGCAGTGTGGGGGCATCCTGGAAATCCACCCTTGTTCGCACGTCGGCCATGTGTTTCCTAAACGGGCTC
CGTATGCCAGGCCCAACTTCCTTCAGAACACGGCACGGGCAGCCGAAGTATGGATGGATGACTACAAAGAGCATTTCTAC
AACAGGAATCCTCCAGCACGGAAGGAAAACTTTGGCGATCTCTCTGAGAGAAAACTCCTCAGAAAGAAGTTGCAGTGCAA
TAACTTTGACTGGTATTTAAAAAACATATTCCCCAATTTGCACGTGCCGGAGGATCGTCCCGGCTGGCATGGGGCCATCC
GCAGCATGGGCATCTCCTCCGAGTGTCTAGACTACAATTCACCGGAACACAATCCTACGGGGGCCCACGTGAGTCTCTTT
GGTTGCCACGGCCAAGGGGGCAACCAATTTTTTGAGTATACGGTGAATCAAGAAATCAGATTTAACTCTGTGACTGAGCT
TTGTGCCGAGGTGCCTGAACAAAAGGATTTTGTAGGCATGAGGACATGCCCAAAAGATGGCACTTTCATTCCAGAAACCA
TTAAATGGCAATTTAGAGAAGATGGAACCATTTATCATCCCCATTCAGCTAAATGCCTTAGTGCTTATCGTACTCCTGAG
GGGCGAGCTGATATTCAGATGACGGCATGTAACGCTGGAGATAAAAATCAAGCGTGGAAGTTTGAGAAATAG

ORF - retro_acar_54 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 63.03 %
Parental protein coverage: 83.61 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalLRRPVYEKPPLGRETELGELGRAARLELSESELRRQEESVALHQINVYLSDRISLHRRLPERRHPQCTEK
L.RPVY.K.P......LGE.G.AARL.LS..E....EE.V....IN.YLSD.ISLHR.....R.P.C..K
RetrocopyLARPVYQK-PPPDPHGLGEWGKAARLTLSPEEKKLEEELVERYAINIYLSDKISLHRHIDDGRMPECRSK
ParentalRYDYYNLPKTSVIIAFYNEAWSTLLRTVHSVLETSPDILLEEIILVDDYSDKEHLKEKLENYVANLRKVR
.YDY..LP.TSVIIAFYNEAWSTLLRT.HSVLE.SP..LL.EIILVDD.SDK..LK..LE.Y..NL..VR
RetrocopyTYDYRRLPTTSVIIAFYNEAWSTLLRTIHSVLESSPSVLLKEIILVDDLSDKVYLKGELEKYISNLQRVR
ParentalLIRANKREGLVRARLLGASIAKGDVLTFLDCHCECHEEWLEPLLERIKEEPSAVVCPVIDVIDWNTFEYL
LIR.NKREGLVRARL.GA..A.GDVLTFLDCHCEC...WLEPLL.R..E..S...CPVID.IDWNTFE..
RetrocopyLIRTNKREGLVRARLIGATFATGDVLTFLDCHCECVPGWLEPLLQRVAENESVIICPVIDTIDWNTFEFY
ParentalGNAGEPQIGGFDWRLVFTWHVVPEREQKQRRSKTDVIRSPTMAGGLFAVNKNYFSYLGSYDTGMEVWGGE
...GEP.IGGFDWRL.F.WH.VP..E...R.SK.D.IRSPTMAGGLFAV.K.YF.YLG.YD.GM.VWGGE
RetrocopyMQPGEPMIGGFDWRLTFQWHSVPDYERQRRKSKVDPIRSPTMAGGLFAVSKKYFEYLGTYDMGMDVWGGE
ParentalNLEFSFRIWQCGGSLEIHPCSHVGHVFPKQAPYSRAKALANSVRAAEVWMDSYKELYYHRNPHARMEPYG
NLE.SFR.WQCGG.LEIHPCSHVGHVFPK.APY.R...L.N..RAAEVWMD.YKE..Y.RNP.AR.E..G
RetrocopyNLELSFRVWQCGGILEIHPCSHVGHVFPKRAPYARPNFLQNTARAAEVWMDDYKEHFYNRNPPARKENFG
ParentalDVTERRLLREKLKCKDFKWYLDNIYPELHVPEDRLGYFGMLKNKGMANFCFDYNPPNEHDITGHVVILYP
D..ER.LLR.KL.C..F.WYL.NI.P.LHVPEDR.G..G.....G....C.DYN.P.EH..TG..V.L..
RetrocopyDLSERKLLRKKLQCNNFDWYLKNIFPNLHVPEDRPGWHGAIRSMGISSECLDYNSP-EHNPTGAHVSLFG
ParentalCHGMGQNQFFEYTSYHEIRYNTRHPEACAAVDPGTDYLKMYLCQDDIQKIPENQKFMLREDGTLVHMQTL
CHG.G.NQFFEYT...EIR.N....E.CA.V....D...M..C..D...IPE..K...REDGT..H....
RetrocopyCHGQGGNQFFEYTVNQEIRFNS-VTELCAEVPEQKDFVGMRTCPKDGTFIPETIKWQFREDGTIYHPHSA
ParentalKCLQA
KCL.A
RetrocopyKCLSA

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 2 .07 RPM 31 .54 RPM
SRP009831_brain 3 .12 RPM 12 .92 RPM
SRP009831_dewlap 4 .01 RPM 44 .89 RPM
SRP009831_embryo 4 .98 RPM 24 .10 RPM
SRP009831_heart 12 .76 RPM 14 .06 RPM
SRP009831_liver 1 .55 RPM 33 .70 RPM
SRP009831_lung 21 .06 RPM 51 .33 RPM
SRP009831_ovary 4 .25 RPM 38 .03 RPM
SRP009831_skeletal_muscle 1 .49 RPM 3 .68 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_54 retrocopy.

TSS - click to see more details

Anolis carolinensis was not studied using FANTOM5 data.

Lab - click to see more details

retro_acar_54 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 33 parental genes, and 37 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG00000002302 1 retrocopy
retro_acar_54 ,
Ailuropoda melanoleuca ENSAMEG000000045201 retrocopy
retro_amel_93,
Anas platyrhynchos ENSAPLG000000121971 retrocopy
retro_apla_8,
Bos taurus ENSBTAG000000090371 retrocopy
retro_btau_1410,
Canis familiaris ENSCAFG000000024941 retrocopy
retro_cfam_683,
Cavia porcellus ENSCPOG000000124181 retrocopy
retro_cpor_1467,
Equus caballus ENSECAG000000165461 retrocopy
retro_ecab_52,
Ficedula albicollis ENSFALG000000051881 retrocopy
retro_falb_8,
Felis catus ENSFCAG000000088311 retrocopy
retro_fcat_126,
Gorilla gorilla ENSGGOG000000057921 retrocopy
retro_ggor_890,
Loxodonta africana ENSLAFG000000220111 retrocopy
retro_lafr_536,
Meleagris gallopavo ENSMGAG000000072441 retrocopy
retro_mgal_1,
Microcebus murinus ENSMICG000000110751 retrocopy
retro_mmur_282,
Myotis lucifugus ENSMLUG000000026301 retrocopy
retro_mluc_804,
Macaca mulatta ENSMMUG000000195611 retrocopy
retro_mmul_888,
Mustela putorius furoENSMPUG000000065021 retrocopy
retro_mputfur_569,
Mus musculus ENSMUSG000000397741 retrocopy
retro_mmus_183,
Nomascus leucogenys ENSNLEG000000170191 retrocopy
retro_nleu_940,
Oryctolagus cuniculus ENSOCUG000000162211 retrocopy
retro_ocun_1260,
Otolemur garnettii ENSOGAG000000014082 retrocopies
retro_ogar_3253, retro_ogar_717,
Ochotona princeps ENSOPRG000000060292 retrocopies
retro_opri_121, retro_opri_515,
Procavia capensis ENSPCAG000000050681 retrocopy
retro_pcap_63,
Pongo abelii ENSPPYG000000194371 retrocopy
retro_pabe_949,
Pelodiscus sinensis ENSPSIG000000172461 retrocopy
retro_psin_1,
Pan troglodytes ENSPTRG000000211801 retrocopy
retro_ptro_777,
Pteropus vampyrus ENSPVAG000000087741 retrocopy
retro_pvam_1347,
Rattus norvegicus ENSRNOG000000080993 retrocopies
retro_rnor_1084, retro_rnor_1085, retro_rnor_2453,
Sarcophilus harrisii ENSSHAG000000174741 retrocopy
retro_shar_44,
Sus scrofa ENSSSCG000000053791 retrocopy
retro_sscr_32,
Ictidomys tridecemlineatus ENSSTOG000000213061 retrocopy
retro_itri_41,
Tupaia belangeri ENSTBEG000000036271 retrocopy
retro_tbel_2065,
Tarsius syrichta ENSTSYG000000049751 retrocopy
retro_tsyr_386,
Tursiops truncatus ENSTTRG000000108481 retrocopy
retro_ttru_212,




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