RetrogeneDB ID:

retro_etel_2004

Retrocopy
location
Organism:Lesser hedgehog tenrec (Echinops telfairi)
Coordinates:scaffold_323901:4970..5704(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS6
Ensembl ID:ENSETEG00000001584
Aliases:None
Description:ribosomal protein S6 [Source:HGNC Symbol;Acc:10429]


Retrocopy-Parental alignment summary:






>retro_etel_2004
AAGCGGAACATCTCCCCAGCCACTAGCTGCCAGAAACTCACTGAGGTGGACAATGAAGGCAAACTTCACACCTTTTATGA
GAAGTGAATGGTTCCAGAAGTTGCTGCCATGTGCGGGGTGATGAAAAGAAGGGTTATATTGTTTGCATCAGTGGTAGGGA
CAACAAGCAAGGTTTTCTCTTGCATCAAGGTGTCTTGAGCCAAGGCCACATCTGTCTGCTGCTGAGTAAGGGGCACTCCT
GTTACAGACCAAAGAGAACTGGGAAGAGGACGCACAGATCTGTCTCGGGTTCACTGCGGATGCAAATCTGAGTGTTCTCA
ACTTGGTTATTGTAAAAAAGGGGGGAGAAAGATAGCCCAGGACTGACTGATACACTGTGCCTCATTGCCTGGGGCCCAAA
AGATCAAGCAAAATCTGCGCTCTTGTCTCTCTAAAAAAGATGATGTCCACCAGTATGTTGTGAGAAAGCCCCTGAACAAG
GAGGGTAAGAAACCCAATACTGAAGCACCCAAGATTAACCTTCTCCTGACTCAGCGTGGCCTGCAGCACAAGAACCTGAA
CATCACCCTGAAGAAGCAGTGCACCAAGAAAAACAAGGAGGAGGCTGCCGAATCTGCCAAGTTTTTGGCCCAGTGAATGA
AGGAGGGCAGAGAAAAACATCAGGGAGACATTACCAAGCCTCAGAGACGGTCCTCTCTGAGAGCTCTACCTTTAAGTCTG
AGTCTAGTCCAAAG

ORF - retro_etel_2004 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 67.32 %
Parental protein coverage: 99.6 %
Number of stop codons detected: 2
Number of frameshifts detected 6


Retrocopy - Parental Gene Alignment:

ParentalKLNISFPATGCQKLIEVDDERKLRTFYEKRMATEVAA-EALGDEWKGYVVRISGGNDKQGFPMKQGVLTH
K.NIS.PAT.CQKL.EVD.E.KL.TFYEK.M..EVAA....GDE.KGY.V.ISG...KQGF...QGVL..
RetrocopyKRNIS-PATSCQKLTEVDNEGKLHTFYEK*MVPEVAA<HVRGDEKKGYIVCISGRDNKQGFLLHQGVLSQ
ParentalGRVRLLLSKGHSCYRPRRTGERKRKSVRGCI-VDANLSVLNLVIVKK-GEKDIPGLTDT-TVPRRLGLKR
G...LLLSKGHSCYRP.RTG.R...SV.G....DANLSVLNLVIVKK.GEKD.PGLTDT.TVP..LG.KR
RetrocopyGHICLLLSKGHSCYRPKRTGKRTHRSVSGSL<ADANLSVLNLVIVKK>GEKDSPGLTDT<TVPHCLGPKR
ParentalASRIRKLFNL-SKEDDVRQYVVRKPLNKEGKKPRTKAPKIQRLVTPRVLQHKRRRIALKKQRTKKNKEEA
.S.I..L..L..K.D.V.QYVVRKPLNKEGKKP.T.APKI..L.T.R.LQHK...I.LKKQ.TKKNKEEA
RetrocopySSKICALVSL<KKDD-VHQYVVRKPLNKEGKKPNTEAPKINLLLTQRGLQHKNLNITLKKQCTKKNKEEA
ParentalAEYAKLLAKRMKEAKEKRQEQIAKRRRLSSLRA-STSKSESSQK
AE.AK.LA..MKE..EK.Q..I.K..R.SSLRA.ST.KSESS.K
RetrocopyAESAKFLAQ*MKEGREKHQGDITKPQRRSSLRA<STFKSESSPK

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_2004 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 14 parental genes, and 132 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000176341 retrocopy
Cavia porcellus ENSCPOG000000037504 retrocopies
Echinops telfairi ENSETEG00000001584 18 retrocopies
Ficedula albicollis ENSFALG000000030781 retrocopy
Homo sapiens ENSG0000013715416 retrocopies
Loxodonta africana ENSLAFG000000107664 retrocopies
Myotis lucifugus ENSMLUG0000000758827 retrocopies
Monodelphis domestica ENSMODG000000040951 retrocopy
Ochotona princeps ENSOPRG000000122905 retrocopies
Pan troglodytes ENSPTRG0000003915319 retrocopies
Rattus norvegicus ENSRNOG0000000766321 retrocopies
Sorex araneus ENSSARG000000065496 retrocopies
Sarcophilus harrisii ENSSHAG000000054861 retrocopy
Tarsius syrichta ENSTSYG000000085698 retrocopies



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