RetrogeneDB ID:

retro_cfam_1975

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:9:20333089..20333331(+)
Located in intron of:ENSCAFG00000014890
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:SNRPF
Ensembl ID:ENSCAFG00000006395
Aliases:None
Description:small nuclear ribonucleoprotein polypeptide F [Source:HGNC Symbol;Acc:11162]


Retrocopy-Parental alignment summary:






>retro_cfam_1975
AATCCGAAACCTTTTCTGAATGGATTAACAGGAAAGCCAGTAACGGTGAAACTGAAGTGGGGAATGGAGTACAAAGGCTA
CCTTGTGTCTGTAGATGGCTATATGAACATGCAGCTTGCAAACACAGAAGAATACATAGATGGAGCGTTGTCTGGACATT
TGGGTGAAGTTTTAATAAGGTGTCATAATGTCCTTTATATCAGGGGTGTGAAGAAGAGTAAGAAGATGGGGAAGTGAGAG
AA

ORF - retro_cfam_1975 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 93.9 %
Parental protein coverage: 72.97 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLGEVLIRCNNVLYIRGV
NPKPFLNGLTGKPV.VKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLGEVLIRC.NVLYIRGV
RetrocopyNPKPFLNGLTGKPVTVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLGEVLIRCHNVLYIRGV
Parental-EEEEEDGEMRE
.EEE.EDGE.RE
Retrocopy<EEE*EDGEVRE

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 10 .96 RPM
SRP017611_brain 0 .00 RPM 3 .97 RPM
SRP017611_kidney 0 .00 RPM 14 .66 RPM
SRP017611_liver 0 .00 RPM 2 .54 RPM
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_1975 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_1975 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_1975 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 12 parental genes, and 34 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000021663 retrocopies
Canis familiaris ENSCAFG00000006395 6 retrocopies
Callithrix jacchus ENSCJAG000000027052 retrocopies
Erinaceus europaeus ENSEEUG000000135094 retrocopies
Echinops telfairi ENSETEG000000015583 retrocopies
Felis catus ENSFCAG000000299664 retrocopies
Latimeria chalumnae ENSLACG000000024561 retrocopy
Loxodonta africana ENSLAFG000000174261 retrocopy
Monodelphis domestica ENSMODG000000080913 retrocopies
Pelodiscus sinensis ENSPSIG000000164622 retrocopies
Sarcophilus harrisii ENSSHAG000000122941 retrocopy
Tarsius syrichta ENSTSYG000000068374 retrocopies



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