RetrogeneDB ID:

retro_btau_1495

Retrocopy
location
Organism:Cow (Bos taurus)
Coordinates:6:62506127..62506524(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSBTAG00000002550
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS12
Ensembl ID:ENSBTAG00000001360
Aliases:None
Description:40S ribosomal protein S12 [Source:UniProtKB/Swiss-Prot;Acc:Q76I81]


Retrocopy-Parental alignment summary:






>retro_btau_1495
GTGGCCGAGGAAGGCATTGCTGCTGGAGGTGTAATAGACGTCAATACTGCTCTGCAAGAGGTGCTGAAGACTGCGCTCAT
CCACGATGGCTTAGCACGTGGAATTGGCGAAGCTGTGAAAGCTTTAGACAAGCGCCAAGCCCATCTACGTGTGCTTGCAT
CCAACCGTGATGAGCCCATGTATGTCAAGTTGGTGGAGGCCCTTTGTGCTGAGCATCAAATCAACCTGATTAAGGTAGAT
GACAACAAGAAACTAGGGGAATGGGTAGGCCTCTGAAAAATTGACAGAGAGGGAAAACCCCGTAAAGTGGTTTGGTTGCA
GTTGTTTGGTGGTTAAGGACTATGGCAAAGAATCTCAGGCCAAGGATGTCATCGAGGAGTACTTCAAATGCAAGAAA

ORF - retro_btau_1495 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 93.23 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMAEEGIAAGGVMDVNTALQEVLKTALIHDGLARGIREAAKALDKRQAHLCVLASNCDEPMYVKLVEALCA
.AEEGIAAGGV.DVNTALQEVLKTALIHDGLARGI.EA.KALDKRQAHL.VLASN.DEPMYVKLVEALCA
RetrocopyVAEEGIAAGGVIDVNTALQEVLKTALIHDGLARGIGEAVKALDKRQAHLRVLASNRDEPMYVKLVEALCA
ParentalEHQINLIKVDDNKKLGEWVGLCKIDREGKPRKVV-GCSCVVVKDYGKESQAKDVIEEYFKCKK
EHQINLIKVDDNKKLGEWVGL.KIDREGKPRKVV.GCSC.VVKDYGKESQAKDVIEEYFKCKK
RetrocopyEHQINLIKVDDNKKLGEWVGL*KIDREGKPRKVV>GCSCLVVKDYGKESQAKDVIEEYFKCKK

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






(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
ERP005899_liver 0 .14 RPM 98 .84 RPM
ERP005899_muscle 1 .16 RPM 1823 .18 RPM
SRP017611_brain 0 .27 RPM 124 .61 RPM
SRP017611_kidney 0 .53 RPM 325 .76 RPM
SRP017611_liver 0 .53 RPM 165 .51 RPM
SRP030211_testis 0 .62 RPM 78 .42 RPM
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_1495 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_1495 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_btau_1495 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 36 parental genes, and 363 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000104791 retrocopy
Ailuropoda melanoleuca ENSAMEG000000080152 retrocopies
Bos taurus ENSBTAG00000001360 7 retrocopies
Canis familiaris ENSCAFG0000000019015 retrocopies
Callithrix jacchus ENSCJAG0000000286534 retrocopies
Cavia porcellus ENSCPOG000000004294 retrocopies
Dasypus novemcinctus ENSDNOG0000000621431 retrocopies
Equus caballus ENSECAG000000015998 retrocopies
Echinops telfairi ENSETEG0000000685414 retrocopies
Felis catus ENSFCAG000000284027 retrocopies
Homo sapiens ENSG0000011230626 retrocopies
Gorilla gorilla ENSGGOG0000001223422 retrocopies
Gadus morhua ENSGMOG000000194551 retrocopy
Loxodonta africana ENSLAFG0000000793311 retrocopies
Macropus eugenii ENSMEUG000000042851 retrocopy
Microcebus murinus ENSMICG000000052525 retrocopies
Myotis lucifugus ENSMLUG000000011375 retrocopies
Macaca mulatta ENSMMUG000000132371 retrocopy
Monodelphis domestica ENSMODG000000175201 retrocopy
Mustela putorius furoENSMPUG000000147711 retrocopy
Mus musculus ENSMUSG000000619831 retrocopy
Nomascus leucogenys ENSNLEG000000146114 retrocopies
Oryctolagus cuniculus ENSOCUG0000000160614 retrocopies
Otolemur garnettii ENSOGAG0000000130920 retrocopies
Pongo abelii ENSPPYG0000001702026 retrocopies
Pelodiscus sinensis ENSPSIG000000034571 retrocopy
Pan troglodytes ENSPTRG0000001861825 retrocopies
Pteropus vampyrus ENSPVAG0000001720112 retrocopies
Rattus norvegicus ENSRNOG000000164115 retrocopies
Sorex araneus ENSSARG000000031702 retrocopies
Sarcophilus harrisii ENSSHAG000000089056 retrocopies
Sus scrofa ENSSSCG000000041778 retrocopies
Tarsius syrichta ENSTSYG0000001009724 retrocopies
Tursiops truncatus ENSTTRG0000000060911 retrocopies
Vicugna pacos ENSVPAG000000100824 retrocopies
Vicugna pacos ENSVPAG000000115043 retrocopies



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