RetrogeneDB ID:

retro_cfam_667

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:15:50292131..50292428(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCAFG00000008160
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SCOC
Ensembl ID:ENSCAFG00000003699
Aliases:None
Description:short coiled-coil protein [Source:HGNC Symbol;Acc:20335]


Retrocopy-Parental alignment summary:






>retro_cfam_667
GACCATTCATCAAGGATTTTGTATCCAAGGCCCAAAAGCTTGTTACCCGAGATGATGAATGCCGACATGGATGCAGTTGA
TGCTAAAAATCAGGTGGAACTGGAGGAAAAAACACGACTCATTAACCAAGTGTTGGAACTGCAACACACACTTGAAGACC
TCTCCGCAAGAGTAGATGCGGTTAAGGAAGAAAATCTGAAGCTAAAATCAGAAAACCAAGTTCTTGGACAATATATAGAA
AACCTCATGTCTGTTTCTAGTGTTTTTCAAACAACTGACACAAAAAGCAAAAGAAAG

ORF - retro_cfam_667 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 95.05 %
Parental protein coverage: 81.45 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalNHSSRILYPRPKSLLPEMMNADMDAVDAENQVELEEKTRLINQVLELQHTLEDTDLSARVDAVKEENLKL
.HSSRILYPRPKSLLPEMMNADMDAVDA.NQVELEEKTRLINQVLELQHTLE..DLSARVDAVKEENLKL
RetrocopyDHSSRILYPRPKSLLPEMMNADMDAVDAKNQVELEEKTRLINQVLELQHTLE--DLSARVDAVKEENLKL
ParentalKSENQVLGQYIENLMSASSVFQTTDTKSKRK
KSENQVLGQYIENLMS.SSVFQTTDTKSKRK
RetrocopyKSENQVLGQYIENLMSVSSVFQTTDTKSKRK

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 6 .34 RPM 32 .00 RPM
SRP017611_brain 5 .40 RPM 33 .82 RPM
SRP017611_kidney 2 .51 RPM 16 .11 RPM
SRP017611_liver 0 .51 RPM 1 .74 RPM
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_667 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_667 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_667 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 23 parental genes, and 62 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000109572 retrocopies
Bos taurus ENSBTAG000000221092 retrocopies
Canis familiaris ENSCAFG00000003699 2 retrocopies
retro_cfam_1564, retro_cfam_667 ,
Choloepus hoffmanni ENSCHOG0000000060410 retrocopies
Callithrix jacchus ENSCJAG000000030602 retrocopies
Dipodomys ordii ENSDORG000000001778 retrocopies
Erinaceus europaeus ENSEEUG000000111071 retrocopy
Homo sapiens ENSG000001531302 retrocopies
Gorilla gorilla ENSGGOG000000281862 retrocopies
Macropus eugenii ENSMEUG000000145342 retrocopies
Macaca mulatta ENSMMUG000000223511 retrocopy
Monodelphis domestica ENSMODG000000255282 retrocopies
Mustela putorius furoENSMPUG000000161192 retrocopies
Nomascus leucogenys ENSNLEG000000050812 retrocopies
Oryctolagus cuniculus ENSOCUG000000065913 retrocopies
Otolemur garnettii ENSOGAG000000264142 retrocopies
Procavia capensis ENSPCAG000000031652 retrocopies
Pongo abelii ENSPPYG000000150772 retrocopies
Pan troglodytes ENSPTRG000000164602 retrocopies
Sarcophilus harrisii ENSSHAG000000034741 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000285293 retrocopies
Tarsius syrichta ENSTSYG000000118146 retrocopies
Tursiops truncatus ENSTTRG000000106771 retrocopy



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