RetrogeneDB ID:

retro_btau_304

Retrocopy
location
Organism:Cow (Bos taurus)
Coordinates:1:88482656..88483382(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSBTAG00000032114
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL7
Ensembl ID:ENSBTAG00000020139
Aliases:None
Description:60S ribosomal protein L7 [Source:UniProtKB/Swiss-Prot;Acc:Q58DT1]


Retrocopy-Parental alignment summary:






>retro_btau_304
GAGGAGAAAAAGAAGATTCTTGCTGTGCCAAAAACCCTTAAGAAAAAGTGAAAGAATTTTGCAGAATTTAAGATCAGGTG
CCTGAGGAAGAAGCTTGCCCAAAAGAAGCTTCAAAAGGCAAGGAGGAAATTTATCTATGAAAAAGCCAAGCAATATCACA
AGGAATACAGGCAGATGTACAGAACGGAAATTCAAATGACTATGGTGGCACAAAAAGTCATCAATCTATGTACCGTGGAA
CCCAAACTGGCATTTGTCATCAGGATCAGAGGTATCAGTGGTGTGAGCACAAAGGTTTGAAAAGTGTTGCAGCTTCTTCA
CCTCTCACAGATCTTCAATGGCACCTTTGTGAAGCTCACCAAGACTTCACTTAACATGCTGGAAACTGTGGAACCATACA
TTGTTTGGGGGTACCCAAATCTAAAGTCCGTAAATGAACTGATCTGCAAGCGTGGCTATGGCAAAATCAACAAGAAGCGA
ATTGCCCTGATGGATAACATGTTGATTGCTCGATCCCCTGGTAAATATGGCATCTTCTGCATGGAGGATCTGATTCATGA
GATCTGTACTGTTGGAAACTGTTTCAAAGAAGGAAACAACTTCCTGTGGCCCTTCAAACTGTCTTCTCCACAAGGTGGAA
TGAAGAAAAAGACCACCCATTTTGTAGAAAGCGGAAATGCTGACAACAGGGAAGACCAGATCAACAGGCTTATTACAAGG
ATGAAC

ORF - retro_btau_304 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 79.42 %
Parental protein coverage: 97.98 %
Number of stop codons detected: 2
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalEKKKKVPAVPETLKKKRKNFAELKIKRLRKKFAQKMLRKARRKLIYEKAKHYHKEYRQMYRTEIRMARMA
E.KKK..AVP.TLKKK.KNFAE.KI..LRKK.AQK.L.KARRK.IYEKAK.YHKEYRQMYRTEI.M...A
RetrocopyEEKKKILAVPKTLKKK*KNFAEFKIRCLRKKLAQKKLQKARRKFIYEKAKQYHKEYRQMYRTEIQMTMVA
ParentalRKAGNFYVPAEPKLAFVIRIRGINGVSPKVRKVLQLLRLRQIFNGTFVKLNKASINMLRIVEPYIAWGYP
.K..N.....EPKLAFVIRIRGI.GVS.KV.KVLQLL.L.QIFNGTFVKL.K.S.NML..VEPYI.WGYP
RetrocopyQKVINLCT-VEPKLAFVIRIRGISGVSTKV*KVLQLLHLSQIFNGTFVKLTKTSLNMLETVEPYIVWGYP
ParentalNLKSVNELIYKRGYGKINKKRIALTDNALIARSLGKYGIICMEDLIHEIYTVGKRFKEANNFLWPFKLSS
NLKSVNELI.KRGYGKINKKRIAL.DN.LIARS.GKYGI.CMEDLIHEI.TVG..FKE.NNFLWPFKLSS
RetrocopyNLKSVNELICKRGYGKINKKRIALMDNMLIARSPGKYGIFCMEDLIHEICTVGNCFKEGNNFLWPFKLSS
ParentalPRGGMKKKTTHFVEGGDAGNREDQINRLIRRMN
P.GGMKKKTTHFVE.G.A.NREDQINRLI.RMN
RetrocopyPQGGMKKKTTHFVESGNADNREDQINRLITRMN

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 178 .37 RPM
ERP005899_muscle 0 .00 RPM 1258 .39 RPM
SRP017611_brain 0 .00 RPM 104 .47 RPM
SRP017611_kidney 0 .12 RPM 269 .03 RPM
SRP017611_liver 0 .00 RPM 138 .03 RPM
SRP030211_testis 0 .07 RPM 222 .08 RPM
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_304 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_304 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_btau_304 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 19 parental genes, and 255 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000184782 retrocopies
Bos taurus ENSBTAG00000020139 22 retrocopies
Callithrix jacchus ENSCJAG000000076861 retrocopy
Equus caballus ENSECAG000000091881 retrocopy
Homo sapiens ENSG0000014760449 retrocopies
Latimeria chalumnae ENSLACG000000035711 retrocopy
Macropus eugenii ENSMEUG000000163199 retrocopies
Microcebus murinus ENSMICG000000028808 retrocopies
Myotis lucifugus ENSMLUG000000285503 retrocopies
Macaca mulatta ENSMMUG000000051411 retrocopy
Monodelphis domestica ENSMODG000000071364 retrocopies
Mus musculus ENSMUSG0000004371615 retrocopies
Otolemur garnettii ENSOGAG000000039032 retrocopies
Pongo abelii ENSPPYG0000001867150 retrocopies
Rattus norvegicus ENSRNOG0000000699227 retrocopies
Ictidomys tridecemlineatus ENSSTOG0000000458618 retrocopies
Tupaia belangeri ENSTBEG000000023011 retrocopy
Tarsius syrichta ENSTSYG0000000610025 retrocopies
Tursiops truncatus ENSTTRG0000000907416 retrocopies



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