RetrogeneDB ID:

retro_cjac_1381

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:15:18945137..18946031(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCJAG00000020635
Aliases:None
Description:ATP synthase gamma chain [Source:UniProtKB/TrEMBL;Acc:F7I4L8]


Retrocopy-Parental alignment summary:






>retro_cjac_1381
GTGTTCTCTCACGCGGGCATCTCTGGGCTGTCGGCCTGGACCTTTCAGCCGCAATGGATTCAGGTTCGAAATATGGCAAC
TTTGAAAGATATTACCAGGCAACTAAAGTCCATCAAAAACATCCAGAAAATTACCAAGTCTATGAAAATGGTAGCAGCAG
CAAAATATGCCCATGCTGAGAGAGAGCTGAAACCAGCTCGAATATATGGATTGGGATCTTTGGCTCTATATGAGAAAGCT
GATATCAAGGGGCCTGAAGACAAGAAGAAACACCTCCTTATTTGTGTGTCTTCAGATCGAGGACTGTGTGGGGCTATTCA
CTCCTCCATTGCAAAACAGATGAAAAGCGAGGTTGCTACACTAACAGCAGCTGGAAAAGAAGTTATGCTTGTTGGAATTG
GTGACAAAATCAGAGGCATACTTTATAGGACTCATTCTGACCAGTTTCTAGCGGCATTCAAAGAAGTAGGAAGAAAGCCC
CCTACTTTTGGAGATGCGTCAGTCATTGCCCTTGAATTACTGAATTCTGGATATGAATTTGATGAAGGCTCCATCATCTT
TAATTGATTCAGGTCTGCCATCTCCTATAAGACAGAGGAAAAGCCCATCTTTTCCCTTGGTATTACCATTGCAAGTGCTG
AGAGCATGAGTATCTACAATGATATTGATGCTGATGTGCTTCAGAATTACCAGGAATACGGTCTGGCCAACATCATCTAC
TACTCTCTGAAGGAGTCTGCCACTAGTGAGCAGAGTGCCAGGATGACAGCCATGGACAACACCAGCAAGAATGCTTCTGA
GATGATTGACAAATTGACATTGACATTCAACTGTACCCGCCAAGCCGTCATCACAAAGGAGTTGATTGAAATCATCTCTG
GTGCTGCAGCTCTG

ORF - retro_cjac_1381 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 94.3 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMFSRAGVSGLSAWTLQPQWIQVRNMATLKDITRRLKSIKNIQKITKSMKMVAAAKYARAERELKPARIYG
.FS.AG.SGLSAWT.QPQWIQVRNMATLKDITR.LKSIKNIQKITKSMKMVAAAKYA.AERELKPARIYG
RetrocopyVFSHAGISGLSAWTFQPQWIQVRNMATLKDITRQLKSIKNIQKITKSMKMVAAAKYAHAERELKPARIYG
ParentalLGSLALYEKADIKGPEDKKKHLLIGVSSDRGLCGAIHSSIAKQMKSEVATLTAAGKEVMLVGIGDKIRGI
LGSLALYEKADIKGPEDKKKHLLI.VSSDRGLCGAIHSSIAKQMKSEVATLTAAGKEVMLVGIGDKIRGI
RetrocopyLGSLALYEKADIKGPEDKKKHLLICVSSDRGLCGAIHSSIAKQMKSEVATLTAAGKEVMLVGIGDKIRGI
ParentalLYRTHSDQFLAAFKEVGRRPPTFGDASVIALELLNSGYEFDEGSIIFNRFRSVISYKTEEKPIFSLN-TI
LYRTHSDQFLAAFKEVGR.PPTFGDASVIALELLNSGYEFDEGSIIFN.FRS.ISYKTEEKPIFSL..TI
RetrocopyLYRTHSDQFLAAFKEVGRKPPTFGDASVIALELLNSGYEFDEGSIIFN*FRSAISYKTEEKPIFSLGITI
ParentalASAESMSIYDDIDADVLQNYQEYSLANIIYYSLKESTTSEQSARMTAMDNASKNASEMIDKLTLTFNRTR
ASAESMSIY.DIDADVLQNYQEY.LANIIYYSLKES.TSEQSARMTAMDN.SKNASEMIDKLTLTFN.TR
RetrocopyASAESMSIYNDIDADVLQNYQEYGLANIIYYSLKESATSEQSARMTAMDNTSKNASEMIDKLTLTFNCTR
ParentalQAVITKELIEIISGAAAL
QAVITKELIEIISGAAAL
RetrocopyQAVITKELIEIISGAAAL

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(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 .13 RPM 39 .45 RPM
SRP051959_heart 0 .07 RPM 96 .77 RPM
SRP051959_kidney 0 .07 RPM 59 .57 RPM
SRP051959_liver 0 .11 RPM 49 .73 RPM
SRP051959_lung 0 .02 RPM 23 .64 RPM
SRP051959_lymph_node 0 .05 RPM 26 .53 RPM
SRP051959_skeletal_muscle 0 .20 RPM 95 .56 RPM
SRP051959_spleen 0 .08 RPM 23 .97 RPM

ChIP-Seq - click to see more details

Callithrix jacchus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_cjac_1381 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_1381 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_1381 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 21 parental genes, and 43 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000050241 retrocopy
retro_cfam_1781,
Choloepus hoffmanni ENSCHOG000000112293 retrocopies
retro_chof_102, retro_chof_297, retro_chof_673,
Callithrix jacchus ENSCJAG00000020635 7 retrocopies
retro_cjac_1079, retro_cjac_1293, retro_cjac_1381 , retro_cjac_1636, retro_cjac_2506, retro_cjac_4190, retro_cjac_526,
Cavia porcellus ENSCPOG000000105232 retrocopies
retro_cpor_422, retro_cpor_984,
Echinops telfairi ENSETEG000000105491 retrocopy
retro_etel_1406,
Felis catus ENSFCAG000000001961 retrocopy
retro_fcat_818,
Homo sapiens ENSG000001656291 retrocopy
retro_hsap_1415,
Gorilla gorilla ENSGGOG000000097191 retrocopy
retro_ggor_1094,
Macaca mulatta ENSMMUG000000092071 retrocopy
retro_mmul_2254,
Monodelphis domestica ENSMODG000000167201 retrocopy
retro_mdom_1287,
Mus musculus ENSMUSG000000257814 retrocopies
retro_mmus_1122, retro_mmus_2008, retro_mmus_3451, retro_mmus_3644,
Nomascus leucogenys ENSNLEG000000119171 retrocopy
retro_nleu_1836,
Oryctolagus cuniculus ENSOCUG000000046422 retrocopies
retro_ocun_1171, retro_ocun_363,
Otolemur garnettii ENSOGAG000000152422 retrocopies
retro_ogar_1099, retro_ogar_2738,
Procavia capensis ENSPCAG000000049711 retrocopy
retro_pcap_99,
Pongo abelii ENSPPYG000000020761 retrocopy
retro_pabe_1170,
Pan troglodytes ENSPTRG000000022771 retrocopy
retro_ptro_968,
Pteropus vampyrus ENSPVAG000000065123 retrocopies
retro_pvam_1466, retro_pvam_51, retro_pvam_530,
Ictidomys tridecemlineatus ENSSTOG000000261331 retrocopy
retro_itri_665,
Tupaia belangeri ENSTBEG000000115304 retrocopies
retro_tbel_1763, retro_tbel_2023, retro_tbel_4384, retro_tbel_4406,
Tarsius syrichta ENSTSYG000000030354 retrocopies
retro_tsyr_1268, retro_tsyr_1988, retro_tsyr_465, retro_tsyr_506,


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