RetrogeneDB ID:

retro_shar_800

Retrocopy
location
Organism:Tasmanian devil (Sarcophilus harrisii)
Coordinates:GL864882.1:1358856..1359403(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL17
Ensembl ID:ENSSHAG00000003060
Aliases:None
Description:ribosomal protein L17 [Source:HGNC Symbol;Acc:10307]


Retrocopy-Parental alignment summary:






>retro_shar_800
AAAATGATGCAGTACTCTATTGATCCAAAGAACTCCACAAAATCATGTAAGTCAAGAGGTTCGTATCTCTGGGTCCACTT
CAAGAATATTCCTGAAACAGCCCAAAATACCAAGGGCATGCATATCTGAAAAGCTACCAACTATTTCAGTGTCACACTGA
AGAGCACAATATATTCCTTTCCATTGATATAATGGTGGAGTTGACAGGTATGCCTAGGCTAAAAAATGGGGTAGAATACA
GAGTCAATGGTCCAAAAAGAGTGTTGAATTCTTGCCGTATATGCTTAAAATGCAGATAGTAATGAGGAACTGAAGAATTT
GGATATAGATTCTCTTGCCATTGAGCATATCCAGTAATAAGGTTCCCAAAATGTGAAGGTATACTTAGAGAGTCCATAGT
CGAATCAACCCATATATGAGTTCTTGCCATATTGAGATGATACTTACTGGAAAGGAACAAATTGTTCCCAAGGTGGAAGA
GGAGATTGCTCAAAAGAAAAAGATATCCTCCCCCAAATAGGAGAAACAAAAGCTTATGGCACAGGAA

ORF - retro_shar_800 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 68.78 %
Parental protein coverage: 100. %
Number of stop codons detected: 6
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalKMVRYSLDPENPTKSCKSRGSNLRVHFKNTRETAQAIKGMHIRKATKYLKDVTLKK-QCVPFRRYNGGVG
KM..YS.DP.N.TKSCKSRGS.L.VHFKN..ETAQ..KGMHI.KAT.Y...VTLK..Q..PF..YNGGV.
RetrocopyKMMQYSIDPKNSTKSCKSRGSYLWVHFKNIPETAQNTKGMHI*KATNYF-SVTLKS>QYIPFH*YNGGVD
ParentalRCAQAKQWGWTQGRWPKKSAEFLLHMLK-NAESNAELKGLDVDSLVIEHIQ-VNKAPK-MRRRTYRAHGR
R.A.AK.WG..Q..W.KKS.EFL..MLK.NA.SN.ELK.LD.DSL.IEHIQ.V...PK.M.R.T.R.H.R
RetrocopyRYA*AKKWGRIQSQWSKKSVEFLPYMLK<NADSNEELKNLDIDSLAIEHIQ<VIRFPK<M*RYT*RVHSR
ParentalINPYMSSPCHIEMILTEKEQIVPKPEEEVAQKKKISQKKLKKQKLMARE
INPYMSS.CHIEMILT.KEQIVPK.EEE.AQKKKIS..K..KQKLMA.E
RetrocopyINPYMSS-CHIEMILTGKEQIVPKVEEEIAQKKKISSPK*EKQKLMAQE

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






Sarcophilus harrisii was not studied using RNA-Seq expression data.
Sarcophilus harrisii was not studied using ChIP-Seq data.
Sarcophilus harrisii was not studied using EST data.
Sarcophilus harrisii was not studied using FANTOM5 data.
retro_shar_800 was not experimentally validated.

Retrocopy orthology:
Sarcophilus harrisii 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 22 parental genes, and 459 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG0000000949840 retrocopies
Bos taurus ENSBTAG000000229025 retrocopies
Canis familiaris ENSCAFG000000190447 retrocopies
Callithrix jacchus ENSCJAG000000047794 retrocopies
Cavia porcellus ENSCPOG0000001933731 retrocopies
Echinops telfairi ENSETEG0000001132210 retrocopies
Felis catus ENSFCAG0000001134243 retrocopies
Homo sapiens ENSG000002154721 retrocopy
Gorilla gorilla ENSGGOG000000266971 retrocopy
Latimeria chalumnae ENSLACG000000088351 retrocopy
Macropus eugenii ENSMEUG0000001670926 retrocopies
Myotis lucifugus ENSMLUG0000002555422 retrocopies
Myotis lucifugus ENSMLUG0000002926436 retrocopies
Macaca mulatta ENSMMUG0000001883726 retrocopies
Monodelphis domestica ENSMODG0000000353411 retrocopies
Mustela putorius furoENSMPUG000000008017 retrocopies
Mus musculus ENSMUSG0000006232880 retrocopies
Oryctolagus cuniculus ENSOCUG000000124852 retrocopies
Pongo abelii ENSPPYG0000000915143 retrocopies
Rattus norvegicus ENSRNOG0000001868048 retrocopies
Sarcophilus harrisii ENSSHAG00000003060 14 retrocopies
Vicugna pacos ENSVPAG000000095681 retrocopy



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