RetrogeneDB ID:

retro_cjac_3160

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:8:100553567..100554451(-)
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:ENSCJAG00000009675
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_3160
GTGTCAGGAGCCCTTGAGGTCCTCCAAATGAAGGAGGAAGATGTCCTTAAGTTCCCGGCAGCAGGAATCCAATTAGCTGG
CACCAACCTTGACTTCCAGATGGAACAGTATATCTATAAAAGGAAAAGTGATGGCATCTACCTCATAAATCTGAAGAGGA
CCTGGGAGCCACTTCTCCTGGCAGCTGGTGCCATTGTTGCCATTGAAAACCCTGCTGATGTCAGTGTTATATCCTCCAGG
AATACTGGCCAGAGGGCCATGCTGAAGTTTGCTGTTGCCACTGGAGCCACTCCAATTGCTGCCGCTTCACTCCTGGAACC
TTCACCAACCAGATCCAGGCAGTCTTCTGGGAGCCACAGTTGCTTGTAGTTACTAACCCAAGGGCTGACCACCAACCTCT
CATGGAGGCATCTTATGTTAACGTACCTACCATTGCTCTGTGCAACACAGATTCTCCTCTGCGCTATGTGGACATTGCCA
TCCCATGTAACAACAATGGAGCTCACTCAGTGGGTTGGATGTGGTGGATGCTGGCTTGAGAAGTTTTGCGCATGCATGGC
ACCATTTCCCGTGAACACCCATGGGAGGTCATGCCTGATCTCTACTTCTACAGAGATCCTGAAGAGATTGAAAAAGAAGA
GCAGGCTGCTGCTGAAAAGGCTCTGACCAAGGAGGAATTTCAAGGCAAATGGACTGCTCGAGCTCCTGAGTTCATTGCTA
CTCAGCCTGAGGTTGCTGACTGGTCTGAAGGCATGCAGGTGCCCTCTGTGCCTATCCAGCAGTTCCCCACTGAAGACCGG
CGTGCTCAACCTGCCACGGAAGACTGGTCTGCAGCTCCCACTGCTCAGGCCACTGAATGGGTAGGAGCAACCTCTGAATG
GTCT

ORF - retro_cjac_3160 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 89.53 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMSGALDVLQMKEEDVLKFLAAGTHLGGTNLDFQMEQYIYKRKSDGIYIINLKRTWEKLLLAARAIVAIEN
.SGAL.VLQMKEEDVLKF.AAG..L.GTNLDFQMEQYIYKRKSDGIY.INLKRTWE.LLLAA.AIVAIEN
RetrocopyVSGALEVLQMKEEDVLKFPAAGIQLAGTNLDFQMEQYIYKRKSDGIYLINLKRTWEPLLLAAGAIVAIEN
ParentalPADVSVISSRNTGQRAVLKFAAATGATPIAG-RFTPGTFTNQIQAAFREPRLLVVTDPRADHQPLTEASY
PADVSVISSRNTGQRA.LKFA.ATGATPIA..RFTPGTFTNQIQA.F.EP.LLVVT.PRADHQPL.EASY
RetrocopyPADVSVISSRNTGQRAMLKFAVATGATPIAA<RFTPGTFTNQIQAVFWEPQLLVVTNPRADHQPLMEASY
ParentalVNLPTIALCNTDSPLRYVDIAIPCNNKGAHSVGLMWWMLAREVLRMRGTISREHPWEVMPDLYFYRDPEE
VN.PTIALCNTDSPLRYVDIAIPCNN.GAHSVG.MWWMLA.EVLRM.GTISREHPWEVMPDLYFYRDPEE
RetrocopyVNVPTIALCNTDSPLRYVDIAIPCNNNGAHSVGWMWWMLA*EVLRMHGTISREHPWEVMPDLYFYRDPEE
ParentalIEKEEQAAAEKAVTKEEFQGEWTAPAPEFTATQPEVADWSEGVQVPSVPIQQFPTEDWSAQPATEDWSAA
IEKEEQAAAEKA.TKEEFQG.WTA.APEF.ATQPEVADWSEG.QVPSVPIQQFPTED..AQPATEDWSAA
RetrocopyIEKEEQAAAEKALTKEEFQGKWTARAPEFIATQPEVADWSEGMQVPSVPIQQFPTEDRRAQPATEDWSAA
ParentalPTAQATEWVGATTEWS
PTAQATEWVGAT.EWS
RetrocopyPTAQATEWVGATSEWS

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 .02 RPM 153 .51 RPM
SRP051959_heart 0 .02 RPM 72 .09 RPM
SRP051959_kidney 0 .00 RPM 95 .00 RPM
SRP051959_liver 0 .00 RPM 179 .07 RPM
SRP051959_lung 0 .00 RPM 106 .96 RPM
SRP051959_lymph_node 0 .00 RPM 200 .13 RPM
SRP051959_skeletal_muscle 0 .00 RPM 118 .32 RPM
SRP051959_spleen 0 .00 RPM 150 .74 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3160 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3160 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_3160 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 27 parental genes, and 426 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000041831 retrocopy
Ailuropoda melanoleuca ENSAMEG0000000896213 retrocopies
Bos taurus ENSBTAG0000000975719 retrocopies
Canis familiaris ENSCAFG0000000510127 retrocopies
Callithrix jacchus ENSCJAG00000009675 15 retrocopies
Dasypus novemcinctus ENSDNOG0000000404827 retrocopies
Dipodomys ordii ENSDORG000000082671 retrocopy
Equus caballus ENSECAG000000130625 retrocopies
Echinops telfairi ENSETEG000000181604 retrocopies
Felis catus ENSFCAG0000000273922 retrocopies
Homo sapiens ENSG000001680282 retrocopies
Loxodonta africana ENSLAFG000000320095 retrocopies
Macropus eugenii ENSMEUG0000000816914 retrocopies
Microcebus murinus ENSMICG0000000451832 retrocopies
Macaca mulatta ENSMMUG0000002296519 retrocopies
Monodelphis domestica ENSMODG000000109672 retrocopies
Mustela putorius furoENSMPUG0000000246321 retrocopies
Mus musculus ENSMUSG000000325181 retrocopy
Nomascus leucogenys ENSNLEG0000000562649 retrocopies
Ochotona princeps ENSOPRG0000000450516 retrocopies
Pan troglodytes ENSPTRG000000228411 retrocopy
Pteropus vampyrus ENSPVAG0000000779419 retrocopies
Rattus norvegicus ENSRNOG0000001864527 retrocopies
Sarcophilus harrisii ENSSHAG000000068962 retrocopies
Tupaia belangeri ENSTBEG0000001594654 retrocopies
Tursiops truncatus ENSTTRG0000001449624 retrocopies
Vicugna pacos ENSVPAG000000123074 retrocopies



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