RetrogeneDB ID:

retro_cjac_854

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:11:53303242..53304475(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCJAG00000014487
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCJAG00000013573
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_854
ATGTCAAAAAGACCATCTTATGCCCCACCTCCCACCCCAGCTCCTGCAACACAAATGCCCAGCACACCAGGGTTTGTGGG
ATACAATCCATACAGTCATCTCGCCTACAACAACTACAGGCTGGGAGGGAACCCGGGCACCAAGAGCCGGGTCACGGCAT
CCTCTGGTATTACGATTCCAAAACCCCCAAAGCCACCAGATAAGCCGCTGATGCCCTACATGAGGTACAGCAGAAAGGTC
TGGGACCAAGTAAAGGCTTCCAACCCTGACCTAAAGTTGTGGGAGATTGGCAAGATTATTGGTGGCATGTGGCGAGATCT
CACTGATGAAGAAAAACAAGAATATTTAAACGAATACGAAGCAGAAAAGATAGAGTACAATGAATCTATGAAGGCCTATC
ATAATTCCCCCGCGTACCTTGCTTACATAAATGCAAAAAGTCGTGCAGAAGCTGCTTTAGAGGAAGAAAGTCGACAGAGA
CAGTCTCGCATGGAGAAAGTAGAACCGTACATCAGCATTCAGCCTGCTGAAGATCCAGATGATTACGATGATGGCTTTTC
AATGAAGCATACAGCCACTGCCCGTTTCCAGAGAAACCACCGCCTCATCAGTGAAATCCTTAGTGAGAGTGTGGTGCCAG
ACGTTCGGTCAGTTGTCACAACAGCTAGAATGCAGGTCCTCAAACGACAGGTCCAGTCCTTAATGGTTCATCAGCGAAAA
CTAGAAGCAGAACTTCTTCAGATAGAGGAACGACACCAGGAGAAGAAGAGGAAATTCCTGGAAAGCACAGATTCGTTTAA
CAATGAACTTAAAAGGTTGTGCGGTCTGAAAGTAGAAGTGGATATGGAGAAAATTGCAGCTGAGATTGCACAGGCAGAGG
AACAGGCCCGCAAAAGGCAGGAGGAAAGGGAGAAGGAGGCAGCAGAGCAAGCTGAACGCAGTCAGAGCAGCATCGTTCCT
GAGGAAGAACAAGCAGCCAACAAAGGCGAGGAGAAGAAGGATGACGAGAACATTCCAATGGAGACAGAGGAGACACACCT
TGAAGAAACGACAGAGAACCAACAAAACGGTGAAGAAGGCACGTCTACTCCTGAGGACAAGGAGAGTGGGCAGGAGGGGG
TCGACAGTATGGCAGAGGAAGGAACCAGTGATAGCAACACTGGCTCGGAGAGCAACAGTGCAACAGTGGAGGAGCCCCCA
ACAGATCCCATACCGGAAGATGAGAAAAAAGAA

ORF - retro_cjac_854 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 99.27 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMSKRPSYAPPPTPAPATQMPSTPGFVGYNPYSHLAYNNYRLGGNPGTNSRVTASSGITIPKPPKPPDKPL
MSKRPSYAPPPTPAPATQMPSTPGFVGYNPYSHLAYNNYRLGGNPGT.SRVTASSGITIPKPPKPPDKPL
RetrocopyMSKRPSYAPPPTPAPATQMPSTPGFVGYNPYSHLAYNNYRLGGNPGTKSRVTASSGITIPKPPKPPDKPL
ParentalMPYMRYSRKVWDQVKASNPDLKLWEIGKIIGGMWRDLTDEEKQEYLNEYEAEKIEYNESMKAYHNSPAYL
MPYMRYSRKVWDQVKASNPDLKLWEIGKIIGGMWRDLTDEEKQEYLNEYEAEKIEYNESMKAYHNSPAYL
RetrocopyMPYMRYSRKVWDQVKASNPDLKLWEIGKIIGGMWRDLTDEEKQEYLNEYEAEKIEYNESMKAYHNSPAYL
ParentalAYINAKSRAEAALEEESRQRQSRMEKGEPYMSIQPAEDPDDYDDGFSMKHTATARFQRNHRLISEILSES
AYINAKSRAEAALEEESRQRQSRMEK.EPY.SIQPAEDPDDYDDGFSMKHTATARFQRNHRLISEILSES
RetrocopyAYINAKSRAEAALEEESRQRQSRMEKVEPYISIQPAEDPDDYDDGFSMKHTATARFQRNHRLISEILSES
ParentalVVPDVRSVVTTARMQVLKRQVQSLMVHQRKLEAELLQIEERHQEKKRKFLESTDSFNNELKRLCGLKVEV
VVPDVRSVVTTARMQVLKRQVQSLMVHQRKLEAELLQIEERHQEKKRKFLESTDSFNNELKRLCGLKVEV
RetrocopyVVPDVRSVVTTARMQVLKRQVQSLMVHQRKLEAELLQIEERHQEKKRKFLESTDSFNNELKRLCGLKVEV
ParentalDMEKIAAEIAQAEEQARKRQEEREKEAAEQAERSQSSIVPEEEQAANKGEEKKDDENIPMETEETHLEET
DMEKIAAEIAQAEEQARKRQEEREKEAAEQAERSQSSIVPEEEQAANKGEEKKDDENIPMETEETHLEET
RetrocopyDMEKIAAEIAQAEEQARKRQEEREKEAAEQAERSQSSIVPEEEQAANKGEEKKDDENIPMETEETHLEET
ParentalTENQQNGEEGTSTPEDKESGQEGVDSMAEEGTSDSNTGSESNSATVEEPPTDPIPEDEKKE
TENQQNGEEGTSTPEDKESGQEGVDSMAEEGTSDSNTGSESNSATVEEPPTDPIPEDEKKE
RetrocopyTENQQNGEEGTSTPEDKESGQEGVDSMAEEGTSDSNTGSESNSATVEEPPTDPIPEDEKKE

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 6 .55 RPM
SRP051959_heart 0 .02 RPM 7 .12 RPM
SRP051959_kidney 0 .11 RPM 9 .32 RPM
SRP051959_liver 0 .02 RPM 4 .98 RPM
SRP051959_lung 0 .05 RPM 10 .59 RPM
SRP051959_lymph_node 0 .05 RPM 10 .25 RPM
SRP051959_skeletal_muscle 0 .00 RPM 4 .50 RPM
SRP051959_spleen 0 .02 RPM 9 .64 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_854 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_854 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_854 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 21 parental genes, and 82 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000160258 retrocopies
Choloepus hoffmanni ENSCHOG000000087273 retrocopies
Callithrix jacchus ENSCJAG00000013573 4 retrocopies
Felis catus ENSFCAG000000096462 retrocopies
Homo sapiens ENSG000000735845 retrocopies
Gorilla gorilla ENSGGOG000000118032 retrocopies
Microcebus murinus ENSMICG000000098214 retrocopies
Myotis lucifugus ENSMLUG000000046091 retrocopy
Macaca mulatta ENSMMUG000000040053 retrocopies
Mustela putorius furoENSMPUG000000146604 retrocopies
Mus musculus ENSMUSG000000379355 retrocopies
Nomascus leucogenys ENSNLEG000000019574 retrocopies
Oryctolagus cuniculus ENSOCUG000000089811 retrocopy
Otolemur garnettii ENSOGAG000000016527 retrocopies
Ochotona princeps ENSOPRG000000009851 retrocopy
Pongo abelii ENSPPYG000000084564 retrocopies
Pan troglodytes ENSPTRG000000229025 retrocopies
Pteropus vampyrus ENSPVAG000000113551 retrocopy
Rattus norvegicus ENSRNOG000000106767 retrocopies
Tupaia belangeri ENSTBEG0000000077010 retrocopies
Tursiops truncatus ENSTTRG000000138851 retrocopy



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