RetrogeneDB ID:

retro_cjac_3213

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:9:42164011..42164335(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:SSR3
Ensembl ID:ENSCJAG00000004643
Aliases:None
Description:signal sequence receptor, gamma (translocon-associated protein gamma) [Source:HGNC Symbol;Acc:11325]


Retrocopy-Parental alignment summary:






>retro_cjac_3213
TTCTCAAATGTCTCATGACATTTGTTCTCAAGCACAACACAGAAGAGGGAGAATGCTGTTTCCAAAGAATTGACTCAAAA
ACTTTCTGAAGCTGATAACAGAAAGATGTCTTGGAAGGAGAAAGATGAAAGAATCTTGTGGAAGGGGAATGAAGTTGCTG
ATTATGAAGCTACATTTTCCATCTTCTATAACAACACTCTGTTCCTGGTCTCAGTCATTGTTGCTTCCTTCTTCACACTG
AAGAAGTTCAACCTCACAGTGAACTACATTTTATCCATAAGTGCTTCATCAGGACTCATCACCCTCCTGTCTACTGGCTC
CAAG

ORF - retro_cjac_3213 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.73 %
Parental protein coverage: 58.92 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalYKNVKFVLKHKVAQKREDAVSKEVTRKLSEADNRKMSRKEKDERILWKKNEVADYEATTFSIFYNNTLFL
..NV...L.....QKRE.AVSKE.T.KLSEADNRKMS.KEKDERILWK.NEVADYEA.TFSIFYNNTLFL
RetrocopyFSNVS*HLFSSTTQKRENAVSKELTQKLSEADNRKMSWKEKDERILWKGNEVADYEA-TFSIFYNNTLFL
ParentalVLVIVASFFILKNFNPTVNYILSISASSGLIALLSTGSK
V.VIVASFF.LK.FN.TVNYILSISASSGLI.LLSTGSK
RetrocopyVSVIVASFFTLKKFNLTVNYILSISASSGLITLLSTGSK

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
SRP051959_colon 0 .00 RPM 58 .38 RPM
SRP051959_heart 0 .00 RPM 46 .50 RPM
SRP051959_kidney 0 .00 RPM 49 .48 RPM
SRP051959_liver 0 .00 RPM 89 .78 RPM
SRP051959_lung 0 .00 RPM 38 .10 RPM
SRP051959_lymph_node 0 .02 RPM 46 .87 RPM
SRP051959_skeletal_muscle 0 .00 RPM 51 .91 RPM
SRP051959_spleen 0 .04 RPM 56 .18 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3213 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3213 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_3213 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 14 parental genes, and 26 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000031251 retrocopy
Canis familiaris ENSCAFG000000088705 retrocopies
Choloepus hoffmanni ENSCHOG000000015171 retrocopy
Callithrix jacchus ENSCJAG00000004643 4 retrocopies
Cavia porcellus ENSCPOG000000058982 retrocopies
Dasypus novemcinctus ENSDNOG000000007522 retrocopies
Homo sapiens ENSG000001148501 retrocopy
Gorilla gorilla ENSGGOG000000240381 retrocopy
Myotis lucifugus ENSMLUG000000154783 retrocopies
Macaca mulatta ENSMMUG000000169701 retrocopy
Otolemur garnettii ENSOGAG000000105892 retrocopies
Pongo abelii ENSPPYG000000142331 retrocopy
Pan troglodytes ENSPTRG000000155601 retrocopy
Tarsius syrichta ENSTSYG000000105781 retrocopy



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