RetrogeneDB ID:

retro_etel_1540

Retrocopy
location
Organism:Lesser hedgehog tenrec (Echinops telfairi)
Coordinates:scaffold_277705:35662..36236(+)
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_1540
ACAGGTAATGGCCTACTGCCGACAGGCGACATCGACGAGGTGGTATATGATGAGGATTCACCTTAGCAGAACATTACAAT
TCTACACTCGGAGCAATTTGGGAAGTTCTCATCCTCAGCGGCGATGATGTTAATTTGGCCGAGAGTGACTTGGCGTATAC
CCGGGCCATTATGGGCAATGGCAAAGAAGAGTACACTGGCAAAGATGTCCTGATTCTGGGCGGTGGCGATGGGGGCGTAT
TATACGAAATAGTGAAACTGAAGCCCAAGATGGTCCCGATGGTAGAGATTGACCAAATGGTGATTGATGGCTGTAAGAAA
TACATGCGAACAATGTGTGGCGAAGTCTAAGACAATCTTAAAGGAGACTGCTATCAGATTCTAATAGCAGACTGCATTCC
CATGCTGAAGAGGTATGCCCAAGAAGGGAGAATGTTTGATTATGTGATTAATGATTTGGACGGCTGTCCCCCATCTCCAT
GTCTCCAGAGGAAGATTCCACCTGGGCGTGTTCTCAAAGTGATTTCTGGACCTTTCAGTGAAAATATGTGAACCAAGAGG
GGGAAATACTTACA

ORF - retro_etel_1540 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.55 %
Parental protein coverage: 54.02 %
Number of stop codons detected: 2
Number of frameshifts detected 6


Retrocopy - Parental Gene Alignment:

ParentalTADGRLVEYDIDEVVYDEDSPYQNIKILHSKQFGN-ILILSGD-VNLAESDMAYTRAIMGSGKEDYTGKD
T..G.L...DIDEVVYDEDSP.QNI.ILHS.QFG...LILSGD.VNLAESD.AYTRAIMG.GKE.YTGKD
RetrocopyTGNGLLPTGDIDEVVYDEDSP*QNITILHSEQFGK<VLILSGDDVNLAESDLAYTRAIMGNGKEEYTGKD
ParentalVLILGGGDGGILCEIVKLKPKMVTMVEIDQMVIDGCKKYMRKTCGEVLDNLKGECYQ-LIADCIPVLKRY
VLILGGGDGG.L.EIVKLKPKMV.MVEIDQMVIDGCKKYMR..CGEV.DNLKG.CYQ.LIADCIP.LKRY
RetrocopyVLILGGGDGGVLYEIVKLKPKMVPMVEIDQMVIDGCKKYMRTMCGEV*DNLKGDCYQILIADCIPMLKRY
ParentalAKEGRMFDYVINDL-TAV-PISTSPEEDSTW-EFLRLI-LDLSMKV-LKQDGKYFT
A.EGRMFDYVINDL.TAV.PIS.SPEEDSTW...L..I.LDLS.K....Q.G...T
RetrocopyAQEGRMFDYVINDL>TAV>PISMSPEEDSTW>RVLKVI>LDLSVKI>VNQEGEILT

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






Echinops telfairi was not studied using RNA-Seq expression data.
Echinops telfairi was not studied using ChIP-Seq data.
Echinops telfairi was not studied using EST data.
Echinops telfairi was not studied using FANTOM5 data.
retro_etel_1540 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
Canis familiaris ENSCAFG000000132843 retrocopies
Callithrix jacchus ENSCJAG000000339331 retrocopy
Cavia porcellus ENSCPOG000000061762 retrocopies
Echinops telfairi ENSETEG00000010098 2 retrocopies
retro_etel_1066, retro_etel_1540 ,
Homo sapiens ENSG000001021725 retrocopies
Gorilla gorilla ENSGGOG000000031233 retrocopies
Microcebus murinus ENSMICG000000001923 retrocopies
Myotis lucifugus ENSMLUG000000131853 retrocopies
Macaca mulatta ENSMMUG000000203922 retrocopies
Monodelphis domestica ENSMODG000000078971 retrocopy
Mus musculus ENSMUSG000000717086 retrocopies
Nomascus leucogenys ENSNLEG000000099554 retrocopies
Oryctolagus cuniculus ENSOCUG000000060162 retrocopies
Pongo abelii ENSPPYG000000201824 retrocopies
Pteropus vampyrus ENSPVAG000000167851 retrocopy
Rattus norvegicus ENSRNOG000000076882 retrocopies
Tupaia belangeri ENSTBEG000000121093 retrocopies
Vicugna pacos ENSVPAG000000075431 retrocopy



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