RetrogeneDB ID:

retro_etel_1066

Retrocopy
location
Organism:Lesser hedgehog tenrec (Echinops telfairi)
Coordinates:scaffold_206303:9023..9918(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:SMS
Ensembl ID:ENSETEG00000010098
Aliases:None
Description:spermine synthase [Source:HGNC Symbol;Acc:11123]


Retrocopy-Parental alignment summary:






>retro_etel_1066
GATGGCGAAACCATTCTCAAAGGCCTGCAGCCCATTTTCCGAGCGCAGGGAATGAGCGAGTCGGTGCACACCTGGCCGGC
CCATGGCTGCTTAGCAACCTACACCAACGAAAATGGCAGCTTTGCCAGTTTGAGAATTTACCCCCACGGCTTGGTGTTGC
TGGACATTCAGAGTTCCGACGGCGATGCGCAAGGCAGCAAAGAACTTGACAGTCTTCTGAACAAAGTAGAAGAACGAATG
AAGGAGCTGAGTCAGCCGAGGGCGCCGAGGGTGAAGCGATTGCCACCCATCGTCCGAGGCGGAGCCGTCGACAGGTACTG
GCCCACTGCCGACGGGCGCCTGGTGGAGTATGACATCGACGAGGTGCTGTATGAGGAGGATTCACCGTATCAGAACATTA
AGATTCTACACTCGAAGCAATTTGGGAATGTTCTCATCCTCAGCGGGGACGTCAATTTGGCCGAGAGTGACGGGGCGTAT
ACCCGGGCCATTATGGGCGGTGGCAACGAAGACTACGCCGGCAAAGACGTCCTGATTCTGGGCGGTGGCGATGGGGGCAT
TTTATGCGAAGTAGTGAAACTGAAGCCCAAGATGGTCACGATGGTAGAGATCGACCAGATGGTGATCGATGCGTGTAAGA
AATTCATGCGCAAAGCATGCGGCGAGGTCTTAGACCACCTTCAAGGGGACTGCTATCGGGTCCTCGTAGCAGACTGCATT
CCTGTCCTGAAGAGGTACGCCCAAGAAGGGAGGATGTTTGATTATGTGATTAATGATTTGACGGCTGTGCCCATCTCCAC
GTCTCCCGAGGAAGATTCCACCTGGGGAGTTTCTCAGACTGATTCTTGACCTTTCAATGAAAGTCTTGAAACACGATGGG
AAATACTTCACACAG

ORF - retro_etel_1066 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.96 %
Parental protein coverage: 85.34 %
Number of stop codons detected: 0
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalDGETILKGLQSIFQEQGMTESVHTWQDHGYLATYTNKNGSFANLRIYPHGLVLLDIQSYDSDAQGNKELD
DGETILKGLQ.IF..QGM.ESVHTW..HG.LATYTN.NGSFA.LRIYPHGLVLLDIQS.D.DAQG.KELD
RetrocopyDGETILKGLQPIFRAQGMSESVHTWPAHGCLATYTNENGSFASLRIYPHGLVLLDIQSSDGDAQGSKELD
ParentalSLLNKIEERMKELNQESTARVKRLPPIVRGGAIDRYWPTADGRLVEYDIDEVVYDEDSPYQNIKILHSKQ
SLLNK.EERMKEL.Q....RVKRLPPIVRGGA.DRYWPTADGRLVEYDIDEV.Y.EDSPYQNIKILHSKQ
RetrocopySLLNKVEERMKELSQPRAPRVKRLPPIVRGGAVDRYWPTADGRLVEYDIDEVLYEEDSPYQNIKILHSKQ
ParentalFGNILILSGDVNLAESDMAYTRAIMGSGKEDYTGKDVLILGGGDGGILCEIVKLKPKMVTMVEIDQMVID
FGN.LILSGDVNLAESD.AYTRAIMG.G.EDY.GKDVLILGGGDGGILCE.VKLKPKMVTMVEIDQMVID
RetrocopyFGNVLILSGDVNLAESDGAYTRAIMGGGNEDYAGKDVLILGGGDGGILCEVVKLKPKMVTMVEIDQMVID
ParentalGCKKYMRKTCGEVLDNLKGECYQ-LIADCIPVLKRYAKEGRMFDYVINDLTAVPISTSPEEDSTW-EFLR
.CKK.MRK.CGEVLD.L.G.CY..L.ADCIPVLKRYA.EGRMFDYVINDLTAVPISTSPEEDSTW.EFLR
RetrocopyACKKFMRKACGEVLDHLQGDCYRVLVADCIPVLKRYAQEGRMFDYVINDLTAVPISTSPEEDSTW>EFLR
ParentalLILDLSMKVLKQDGKYFTQ
LILDLSMKVLK.DGKYFTQ
RetrocopyLILDLSMKVLKHDGKYFTQ

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






RNA-Seq - click to see more details

Echinops telfairi was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Echinops telfairi was not studied using ChIP-Seq data.

EST - click to see more details

Echinops telfairi was not studied using EST data.

TSS - click to see more details

Echinops telfairi was not studied using FANTOM5 data.

Lab - click to see more details

retro_etel_1066 was not experimentally validated.

Retrocopy orthology:
Echinops telfairi 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 49 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000183821 retrocopy
retro_btau_1412,
Canis familiaris ENSCAFG000000132843 retrocopies
retro_cfam_1076, retro_cfam_1995, retro_cfam_613,
Callithrix jacchus ENSCJAG000000339331 retrocopy
retro_cjac_518,
Cavia porcellus ENSCPOG000000061762 retrocopies
retro_cpor_729, retro_cpor_889,
Echinops telfairi ENSETEG00000010098 2 retrocopies
retro_etel_1066 , retro_etel_1540,
Homo sapiens ENSG000001021725 retrocopies
retro_hsap_243, retro_hsap_3168, retro_hsap_3193, retro_hsap_3611, retro_hsap_4826,
Gorilla gorilla ENSGGOG000000031233 retrocopies
retro_ggor_1335, retro_ggor_2437, retro_ggor_3009,
Microcebus murinus ENSMICG000000001923 retrocopies
retro_mmur_1421, retro_mmur_1484, retro_mmur_699,
Myotis lucifugus ENSMLUG000000131853 retrocopies
retro_mluc_471, retro_mluc_530, retro_mluc_92,
Macaca mulatta ENSMMUG000000203922 retrocopies
retro_mmul_2003, retro_mmul_2574,
Monodelphis domestica ENSMODG000000078971 retrocopy
retro_mdom_412,
Mus musculus ENSMUSG000000717086 retrocopies
retro_mmus_2162, retro_mmus_2170, retro_mmus_2837, retro_mmus_3502, retro_mmus_3628, retro_mmus_994,
Nomascus leucogenys ENSNLEG000000099554 retrocopies
retro_nleu_1664, retro_nleu_2200, retro_nleu_2208, retro_nleu_2755,
Oryctolagus cuniculus ENSOCUG000000060162 retrocopies
retro_ocun_1458, retro_ocun_1918,
Pongo abelii ENSPPYG000000201824 retrocopies
retro_pabe_2649, retro_pabe_2810, retro_pabe_3752, retro_pabe_38,
Pteropus vampyrus ENSPVAG000000167851 retrocopy
retro_pvam_524,
Rattus norvegicus ENSRNOG000000076882 retrocopies
retro_rnor_1934, retro_rnor_938,
Tupaia belangeri ENSTBEG000000121093 retrocopies
retro_tbel_1630, retro_tbel_1893, retro_tbel_3570,
Vicugna pacos ENSVPAG000000075431 retrocopy
retro_vpac_50,


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