RetrogeneDB ID:

retro_btau_1318

Retrocopy
location
Organism:Cow (Bos taurus)
Coordinates:4:34601651..34601948(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:UBA52
Ensembl ID:ENSBTAG00000007737
Aliases:UBA52, RPS27A, UBB, UBC
Description:Ubiquitin-60S ribosomal protein L40 Ubiquitin 60S ribosomal protein L40 [Source:UniProtKB/Swiss-Prot;Acc:P63048]


Retrocopy-Parental alignment summary:






>retro_btau_1318
AGGACCATCATCATCGAGGTCAAGTCCAGCGACACCACTGACAATATCAAAGCTAAAATCCAAGACAAGGAGGGCAACTG
GCCTGATTAGCAGCATCTGATTTCCACAGGCAAACAGCTGGAGGATGACAGCACTCTGTCAGATCACAATATCCAGAAAG
AGCCTGCCCGGCTCTTGGTGCTTCGTGTGCAAGCCAGCATCATTGAGCCTTCCCTTTGCCAACTCACTCAGAAATACAGC
GGCAACAAGATGATCTGCTGCGAGTATTGTGCTTGCCTACAGCCCCACGCTGCCCAC

ORF - retro_btau_1318 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 60.61 %
Parental protein coverage: 77.34 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGIIEP
.TI..EV..SDT..N.KAKIQDKEG..PD.Q.LI..GKQLED..TLSD.NIQKE....LVLR....IIEP
RetrocopyRTIIIEVKSSDTTDNIKAKIQDKEGNWPD*QHLISTGKQLEDDSTLSDHNIQKEPARLLVLRVQASIIEP
ParentalSLRQLAQKYNCDKMICRKCYARLHPRAVN
SL.QL.QKY...KMIC....A.L.P.A..
RetrocopySLCQLTQKYSGNKMICCEYCACLQPHAAH

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 .00 RPM 161 .42 RPM
ERP005899_muscle 0 .00 RPM 900 .42 RPM
SRP017611_brain 0 .00 RPM 104 .79 RPM
SRP017611_kidney 0 .00 RPM 167 .15 RPM
SRP017611_liver 0 .00 RPM 152 .07 RPM
SRP030211_testis 0 .00 RPM 228 .14 RPM
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_1318 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_1318 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_btau_1318 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 16 parental genes, and 99 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG0000001135610 retrocopies
Bos taurus ENSBTAG00000007737 3 retrocopies
retro_btau_1059, retro_btau_1318 , retro_btau_832,
Callithrix jacchus ENSCJAG0000000747022 retrocopies
Equus caballus ENSECAG000000206608 retrocopies
Felis catus ENSFCAG0000000974514 retrocopies
Homo sapiens ENSG000002219832 retrocopies
Latimeria chalumnae ENSLACG000000081321 retrocopy
Mustela putorius furoENSMPUG000000155278 retrocopies
Mus musculus ENSMUSG000000901373 retrocopies
Ochotona princeps ENSOPRG000000047846 retrocopies
Pongo abelii ENSPPYG000000097462 retrocopies
Pan troglodytes ENSPTRG000000392238 retrocopies
Rattus norvegicus ENSRNOG000000199747 retrocopies
Sarcophilus harrisii ENSSHAG000000070753 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000046781 retrocopy
Xiphophorus maculatus ENSXMAG000000039111 retrocopy



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