RetrogeneDB ID:

retro_shar_539

Retrocopy
location
Organism:Tasmanian devil (Sarcophilus harrisii)
Coordinates:GL849858.1:3427317..3427708(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL14
Ensembl ID:ENSSHAG00000001591
Aliases:None
Description:ribosomal protein L14 [Source:HGNC Symbol;Acc:10305]


Retrocopy-Parental alignment summary:






>retro_shar_539
CTGGTTAAAGGGGGCTGCAGTGGTATGAAGAATCAAGCTATGCCTTTCAAGTGTATGCAATTCACAAACTTCATTTTCAA
ATTTCCATACAGCACTTGTCAGCAGCATGTCCTGGCTATTTAGGAGAAAGAAAATATTAGATTAAAATGGACAGCTATAG
GATGGGTCAAAAAGATTGAAACTAGAGAAAGGAAAGCCAAAATGACAGATTTTGATCATTAGAAAGTAGTGAAGGCAAGG
CAAATTAGAAAACAAAGTTATCAAGCATGAAATGAAGAAAATGAGAAAATCATTTTCCCTAAAGGAAACTCTTAAAATGG
AATGTACCCAGAAGAGAGCACCTGTCCCAAAAATCCTTGCCAATAAGATCTCCACTAAGAAGATGCTGGGC

ORF - retro_shar_539 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 55.73 %
Parental protein coverage: 74.14 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalLVDGPCSGVRRQAMPFKCMQLTDFVLKFPHSARQKYVRAAWEKEKINTKWKATRWAKKIEARERKAKMTD
LV.G.CSG...QAMPFKCMQ.T.F..KFP.S..Q..V.A..EKE.I..KW.A..W.KKIE.RERKAKMTD
RetrocopyLVKGGCSGMKNQAMPFKCMQFTNFIFKFPYSTCQQHVLAI*EKENIRLKWTAIGWVKKIETRERKAKMTD
ParentalFDRYKVMKAK-KMRNRIIKHEVKKLQKASTQKGSPKKGATQK-ALASKVSAKKIPAKKAEG
FD..KV.KA..K..N..IKHE.KK..K....K...K...TQK.A...K..A.KI..KK..G
RetrocopyFDH*KVVKAR>KLENKVIKHEMKKMRKSFSLKETLKMECTQKRAPVPKILANKISTKKMLG

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_539 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 27 parental genes, and 88 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000017094 retrocopies
Canis familiaris ENSCAFG000000051381 retrocopy
Callithrix jacchus ENSCJAG000000178849 retrocopies
Cavia porcellus ENSCPOG000000007111 retrocopy
Equus caballus ENSECAG000000268132 retrocopies
Echinops telfairi ENSETEG000000128946 retrocopies
Felis catus ENSFCAG000000156554 retrocopies
Homo sapiens ENSG000001888466 retrocopies
Gorilla gorilla ENSGGOG000000259583 retrocopies
Latimeria chalumnae ENSLACG000000156391 retrocopy
Microcebus murinus ENSMICG000000092174 retrocopies
Myotis lucifugus ENSMLUG000000144294 retrocopies
Monodelphis domestica ENSMODG000000152622 retrocopies
Mustela putorius furoENSMPUG000000179611 retrocopy
Mus musculus ENSMUSG000000257943 retrocopies
Nomascus leucogenys ENSNLEG000000056822 retrocopies
Oryctolagus cuniculus ENSOCUG000000103093 retrocopies
Pan troglodytes ENSPTRG000000119634 retrocopies
Pteropus vampyrus ENSPVAG000000139147 retrocopies
Rattus norvegicus ENSRNOG000000190074 retrocopies
Sorex araneus ENSSARG000000039742 retrocopies
Sarcophilus harrisii ENSSHAG00000001591 5 retrocopies
Sus scrofa ENSSSCG000000112722 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000214601 retrocopy
Tarsius syrichta ENSTSYG000000021615 retrocopies
Tursiops truncatus ENSTTRG000000067081 retrocopy
Xenopus tropicalis ENSXETG000000220181 retrocopy



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