RetrogeneDB ID:

retro_cfam_1415

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:30:8640395..8640634(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS23
Ensembl ID:ENSCAFG00000030896
Aliases:None
Description:ribosomal protein S23 [Source:HGNC Symbol;Acc:10410]


Retrocopy-Parental alignment summary:






>retro_cfam_1415
CATTTGGGCACAGTCCTGAAGGCCAACCTTTTTGGAGGCGTTTGCCATGCAAGGGAATTTTGCTGGAAAAAGTAGCAGTT
GAAGCCAAACAGCTAAATTATGCCATCAGGAAGTGTGTCAGAGTCCAGCTGATCAAGAATGGCAGAAAAAAAAAATCAAT
CTTTGTACTCAATGATGGTTGTCTGGAGGAAAATGATGAGATTCTTGTTGTTGAATTTAGTTGTAAAGATCACACTGTC

ORF - retro_cfam_1415 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 69.05 %
Parental protein coverage: 57.34 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalHLGTALKANPFGGASHA-KGIVLEKVGVEAKQPNSAIRKCVRVQLIKNG-KKITAFVPNDGCLNFIEEND
HLGT.LKAN.FGG..HA.KGI.LEKV.VEAKQ.N.AIRKCVRVQLIKNG......FV.NDGCL...EEND
RetrocopyHLGTVLKANLFGGVCHA<KGILLEKVAVEAKQLNYAIRKCVRVQLIKNGXXXXSIFVLNDGCL---EEND
ParentalEVLVAGFGRKGHAV
E.LV..F..K.H.V
RetrocopyEILVVEFSCKDHTV

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
SRP012049_cerebellum 0 .00 RPM 263 .92 RPM
SRP017611_brain 0 .00 RPM 66 .29 RPM
SRP017611_kidney 0 .07 RPM 327 .48 RPM
SRP017611_liver 0 .00 RPM 154 .74 RPM
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_1415 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_1415 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_1415 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 9 parental genes, and 32 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000133583 retrocopies
Canis familiaris ENSCAFG00000030896 7 retrocopies
Callithrix jacchus ENSCJAG000000112472 retrocopies
Dipodomys ordii ENSDORG000000018132 retrocopies
Macropus eugenii ENSMEUG000000129311 retrocopy
Macaca mulatta ENSMMUG000000035784 retrocopies
Pteropus vampyrus ENSPVAG000000020834 retrocopies
Sarcophilus harrisii ENSSHAG000000083472 retrocopies
Vicugna pacos ENSVPAG000000094277 retrocopies



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