RetrogeneDB ID:

retro_shar_340

Retrocopy
location
Organism:Tasmanian devil (Sarcophilus harrisii)
Coordinates:GL841396.1:1600810..1601103(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL9
Ensembl ID:ENSSHAG00000004918
Aliases:None
Description:ribosomal protein L9 [Source:HGNC Symbol;Acc:10369]


Retrocopy-Parental alignment summary:






>retro_shar_340
TTATTTTCCCATCAATGTTCCCCATCGATTATTCAAGAGAATGGCTTACTTGTTAAAATCAGAAATTTCTTGGGTGAAAA
ATATATTTGAAGAGTGTTTATGAAACCAGATATTACTTATGCTGTTTCTCAAATCCAAAAAGATGAGTTAATTCTTGAAG
AAAATAATATTGAACTTGTATTAAACTCAGCTACCCTGGTCCAACAGGCCACTGTGGTCAAAGGAAGGATATCAGAAAAA
TTTTAGATGGTATCTTTGTTTCTGAGAAAGGCACAATGCAACAAGCTGATGAA

ORF - retro_shar_340 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 69.7 %
Parental protein coverage: 51.04 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalVYAHFPINVVIQENGSLVEIRNFLGEKYIRRVRMRPGVACAVSQAQKDELILEGNDIELVSNSAALIQQA
...H......IQENG.LV.IRNFLGEKYI.RV.M.P....AVSQ.QKDELILE.N.IELV.NSA.L.QQA
RetrocopyLFSHQCSPSIIQENGLLVKIRNFLGEKYI*RVFMKPDITYAVSQIQKDELILEENNIELVLNSATLVQQA
ParentalTTVK-NKDIRKFLDGIYVSEKGTVQQADE
T.VK..KDIRK.LDGI.VSEKGT.QQADE
RetrocopyTVVK<RKDIRKILDGIFVSEKGTMQQADE

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_340 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 34 parental genes, and 594 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000073171 retrocopy
Ailuropoda melanoleuca ENSAMEG0000000318731 retrocopies
Bos taurus ENSBTAG000000145183 retrocopies
Canis familiaris ENSCAFG0000001600828 retrocopies
Callithrix jacchus ENSCJAG0000000072329 retrocopies
Cavia porcellus ENSCPOG0000000454315 retrocopies
Danio rerio ENSDARG000000373501 retrocopy
Dasypus novemcinctus ENSDNOG0000000741118 retrocopies
Dipodomys ordii ENSDORG000000010886 retrocopies
Equus caballus ENSECAG000000164897 retrocopies
Erinaceus europaeus ENSEEUG0000000439439 retrocopies
Felis catus ENSFCAG0000001228434 retrocopies
Homo sapiens ENSG0000016368228 retrocopies
Gorilla gorilla ENSGGOG0000002279926 retrocopies
Gadus morhua ENSGMOG000000010021 retrocopy
Loxodonta africana ENSLAFG0000001202138 retrocopies
Macropus eugenii ENSMEUG000000167228 retrocopies
Microcebus murinus ENSMICG0000001677818 retrocopies
Myotis lucifugus ENSMLUG0000000459734 retrocopies
Macaca mulatta ENSMMUG0000000855322 retrocopies
Monodelphis domestica ENSMODG000000205537 retrocopies
Mus musculus ENSMUSG000000472152 retrocopies
Nomascus leucogenys ENSNLEG0000001710026 retrocopies
Otolemur garnettii ENSOGAG0000000493520 retrocopies
Procavia capensis ENSPCAG0000000583422 retrocopies
Pongo abelii ENSPPYG0000001467510 retrocopies
Pteropus vampyrus ENSPVAG0000000091949 retrocopies
Rattus norvegicus ENSRNOG000000267163 retrocopies
Sarcophilus harrisii ENSSHAG00000004918 8 retrocopies
Sus scrofa ENSSSCG0000002519215 retrocopies
Ictidomys tridecemlineatus ENSSTOG0000000207713 retrocopies
Tupaia belangeri ENSTBEG0000000604218 retrocopies
Tursiops truncatus ENSTTRG0000001428913 retrocopies
Vicugna pacos ENSVPAG000000020231 retrocopy



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