RetrogeneDB ID:

retro_itri_59

Retrocopy
location
Organism:Squirrel (Ictidomys tridecemlineatus)
Coordinates:JH393790.1:380585..382088(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSSTOG00000021919
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:GMCL1
Ensembl ID:ENSSTOG00000000714
Aliases:None
Description:germ cell-less, spermatogenesis associated 1 [Source:HGNC Symbol;Acc:23843]


Retrocopy-Parental alignment summary:






>retro_itri_59
ATGGGGATCCTAAGTAGCAGGATCTTGCGATGCAGAGAACCAGGTACCATAGATCTGCAGCAGTCTGAAGCCACAGCGGG
TCCCAGTTACATATCTAGCAGTCGGAAGCGTAAGCAGAGTGGTGGGTATTGTTCAGGTTTAAAATCTGACACCAAGAAGT
TTCAGGACCAGGGAGAAAATCTACAGCAAGTCTTCAGCACCAACCACAGAAAAAAAGTTAAGATTACATCCAAGTATGCT
TACCAAAATTTATTTTTGAATGGAGAAAACAGTGACATCAAAATCCGTGCTCTGGGGAAAATATGGTGTTTACACAAAAT
ATTTTTATATCAATCAGACTACTTTGCTGATATGTTTAGAAGTTCTTGGGAAGAATTGCACAAAGATATTATTGAACTGG
ATATTCGTGACCAGAATATAGATATCCAATCTTTGCACTTTGTACTAGGTTCATTGTATAGGGATGAGTATTTCTTAATA
GAGCCCCTTCAAGTTCCAGGTGTTTTGGCAACATCATATCTGCTTCAGGTAGAGGACTTAATTCAGCAATGTAGTGAAAC
CATGAAAGACACAATTAATGTGAAAACTGTATGTAGTTATTATGCAGCAGCAGAAACCTATGGGTTAGATTCTGTAAAGA
CAGGGTGCTTTGAATGGCTTCTTCACAATTTGATGACACACCCAAGTGCTGAGCTCTACAAAGAAATAGGCATAGAGCTT
ATGGATTTGCTCATCTCTTCCTCTAATTTACTAGTAATACAAAAGGAAATGGATATATACACAACACTTAAAGAGTGGAT
GTTTCTTCATCTTAACCCATCTTGGAAAGGCTCAATGAAACAGCTTCTAATTAATACTAATAATTGGCTTTCTAGACACA
GGGAATGTGGTGGCTATAACACTTTTCTTGACACAGAAGAAGGAATATCATTTAAACCAGTGTTTAAAAAATTGAGGTTT
CAGCATATCATCTGTGACCTGGCCTCAACAAAAGTAATTGAACAAGATGGTCTAATACCTTCAGAGTGGTTGTCATCTGT
TTACAAACAACAATGGCTTACCTTGCTTAAGGCACAACAATACAGGGAGATCGGGCCTCGAGACATCAATGAAACAGAAC
TTGAAGGATACAGCATGAGGTGTGGTAAAAGGATTATCAAAGATGGTAAATATTCCTGGAAGTGGTCAGGTTACAATTTT
GGCTTTCCCTTACATGTTATTTTTGACAGCCATTATATAATTTTCAAGCAAAATACTTTCAGTCAGCTATGTGAAGATTC
TGCCTGCTTACAACCTCTACGAAATATTGCGTTCAGATTAACTTTGGTATATTTTGATGCTAGTGGAAAATTAAATTTCA
GCAAAACAACAGGCTATAAAATACTTACTTTTTCAAAAGATGAGGAACAAGTGGTGATGAAGTTGGATAGCATAGTTCTG
AACTTCCCTTTATATATATTCTGCAACTTCCTATTTATATCATTAGAAAATACAGAAAACTGA

ORF - retro_itri_59 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 59.79 %
Parental protein coverage: 89.92 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalYCPGSRKRKRSSGAFCYCHP-DSETDEDEDEGDEQQRLLNTPRRKKLKSTSKYIYQTLFLNGENSDIKIC
Y...SRKRK.S.G...YC....S.T....D.G...Q....T..RKK.K.TSKY.YQ.LFLNGENSDIKI.
RetrocopyYISSSRKRKQSGG---YCSGLKSDTKKFQDQGENLQQVFSTNHRKKVKITSKYAYQNLFLNGENSDIKIR
ParentalALGEEWSLHKIYLCQSGYFSSMFSGSWKESSMNIIELEIPDQNIDIEALQVAFGSLYRDDV-LIKPSRVI
ALG..W.LHKI.L.QS.YF..MF..SW.E....IIEL.I.DQNIDI..L....GSLYRD...LI.P..V.
RetrocopyALGKIWCLHKIFLYQSDYFADMFRSSWEELHKDIIELDIRDQNIDIQSLHFVLGSLYRDEYFLIEPLQVP
ParentalAILAAACMLQLDGLIQQCGETMKETINVKTVCGYYTSAGIYGLDSVKKKCLEWLLNNLMTHQNVELFKEL
..LA....LQ...LIQQC.ETMK.TINVKTVC.YY..A..YGLDSVK..C.EWLL.NLMTH...EL.KE.
RetrocopyGVLATSYLLQVEDLIQQCSETMKDTINVKTVCSYYAAAETYGLDSVKTGCFEWLLHNLMTHPSAELYKEI
ParentalSINIMKQLIGSSNLFVMQVEMDVYTALKKWMFLQLVPSWNGSLKQLLTETDVWFSKRRKDFEGTAFLETE
.I..M..LI.SSNL.V.Q.EMD.YT.LK.WMFL.L.PSW.GS.KQLL..T..W.S..R.......FL.TE
RetrocopyGIELMDLLISSSNLLVIQKEMDIYTTLKEWMFLHLNPSWKGSMKQLLINTNNWLSRHRECGGYNTFLDTE
ParentalQGKPFVSVFRHLRLQYIISDLASARIIEQDSLVPSEWLSSVYKQQWLAMLRAEQDSEVGPQEINKEELEG
.G..F..VF..LR.Q.II.DLAS...IEQD.L.PSEWLSSVYKQQWL..L.A.Q..E.GP..IN..ELEG
RetrocopyEGISFKPVFKKLRFQHIICDLASTKVIEQDGLIPSEWLSSVYKQQWLTLLKAQQYREIGPRDINETELEG
ParentalNSMRCGRKLAKDGEYCWRWTGFNFGFDLLVTYTNRYIIFKRNTLNQPCSGSVSLQPRRSIAFRLRLASFD
.SMRCG....KDG.Y.W.W.G.NFGF.L.V.....YIIFK.NT..Q.C..S..LQP.R.IAFRL.L..FD
RetrocopyYSMRCGKRIIKDGKYSWKWSGYNFGFPLHVIFDSHYIIFKQNTFSQLCEDSACLQPLRNIAFRLTLVYFD
ParentalSSGKLICSRTTGYQILTLEKDQEQVVMNLDSRLLIFPLYICCNFLYISPEKRTEN
.SGKL..S.TTGY.ILT..KD.EQVVM.LDS..L.FPLYI.CNFL.IS.E..TEN
RetrocopyASGKLNFSKTTGYKILTFSKDEEQVVMKLDSIVLNFPLYIFCNFLFISLE-NTEN

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






RNA-Seq - click to see more details

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_itri_59 retrocopy.

TSS - click to see more details

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_itri_59 was not experimentally validated.

Retrocopy orthology:
Ictidomys tridecemlineatus 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 19 parental genes, and 29 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000161161 retrocopy
retro_amel_1915,
Choloepus hoffmanni ENSCHOG000000123062 retrocopies
retro_chof_1562, retro_chof_802,
Equus caballus ENSECAG000000168132 retrocopies
retro_ecab_1109, retro_ecab_899,
Homo sapiens ENSG000000873381 retrocopy
retro_hsap_3407,
Loxodonta africana ENSLAFG000000025653 retrocopies
retro_lafr_220, retro_lafr_592, retro_lafr_98,
Myotis lucifugus ENSMLUG000000091832 retrocopies
retro_mluc_1521, retro_mluc_31,
Macaca mulatta ENSMMUG000000008581 retrocopy
retro_mmul_98,
Mus musculus ENSMUSG000000011571 retrocopy
retro_mmus_3665,
Nomascus leucogenys ENSNLEG000000101321 retrocopy
retro_nleu_2993,
Oryctolagus cuniculus ENSOCUG000000158082 retrocopies
retro_ocun_112, retro_ocun_160,
Otolemur garnettii ENSOGAG000000084081 retrocopy
retro_ogar_151,
Pongo abelii ENSPPYG000000123341 retrocopy
retro_pabe_209,
Pan troglodytes ENSPTRG000000120211 retrocopy
retro_ptro_2314,
Pteropus vampyrus ENSPVAG000000012423 retrocopies
retro_pvam_1259, retro_pvam_370, retro_pvam_816,
Sorex araneus ENSSARG000000046511 retrocopy
retro_sara_425,
Sus scrofa ENSSSCG000000083351 retrocopy
retro_sscr_62,
Ictidomys tridecemlineatus ENSSTOG00000000714 1 retrocopy
retro_itri_59 ,
Tursiops truncatus ENSTTRG000000074933 retrocopies
retro_ttru_1039, retro_ttru_1647, retro_ttru_1648,
Vicugna pacos ENSVPAG000000017561 retrocopy
retro_vpac_617,


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