RetrogeneDB ID:

retro_cjac_572

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:1:82753551..82755119(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PRRC2A
Ensembl ID:ENSCJAG00000003047
Aliases:None
Description:proline-rich coiled-coil 2A [Source:HGNC Symbol;Acc:13918]


Retrocopy-Parental alignment summary:






>retro_cjac_572
ATGTCAGATCGCTGGGGGCCGACTGCCAAGGGAAATGATGGAAACAAGTATTCCTCGCTCAACCTGTTTGACACATATAA
GGGCAAGTCCTTAGAGATCCAGAAACCGGCTGTTGTCCCTCGCCATGGCCTGCAGAGTCTCAGCAAAGTTGCCATTGCCA
GGCGTATGCCACCTCCAGCCAACCTTCCAAGCCTGAAAGCCGAGAACAAAGGCAATGACCCCAATGTCTCACTAGTGCCG
AAAGACGGAACAGGATAGGCAAGCAAACAGGAGCAGTCCGACCCCAAGAGTTCCGATGCCTCAACCGCTCAGCCACCGGA
ATCGCAGCCACTGCAGGCTCCACCGACGCCTGCCTCCAACCAGCCGAAACGACCCCCAGCAGCCCCGGAGAACACTCCTT
CGGTTGCAAGCGGGGTAAAGTCCTGGGCACAAGTCAGCGTCAGCTATGGAGCACATGGAGATGGTGGAAGGGCATCAAGC
CTACTGTCGCGATTCTCTCGAGAGGAATTTCTGACCCAGCAGGCGGCTGGCGCCCAGAACAAGGCTGCCAAGGAGAGGGA
GTCTGCCAAATAGTCGTCTGGGCCCGGACCAAGCCTCTGCCCCCAAAATTCTACAACTTGGAGGGACGGAGGTGGGCTTG
GCTCTGATGAGCTGGAGGGTCCGGACTCCAAACTTCATCATGGTCATGATCCCCAGGGGGCGCTGCAGCCTTCAGGCCCA
CCCCAGTTCCCTCCCTACCGCGGAATGATGCCGCCTTTCATGTATCCTCCATATCTCCCATTCCCTCCGCCCTATGGACC
CCAGGGGCCTTACCGATACCCAACTCCTGATGGGCCCAGCCGTTTTCCCCATGTGGCGGGCCCCCGAGGGTCAGGGCCAC
CAATACGCCTAGTAGAGCCTGTGGGTCATCCCTCTATTCTCAAAGAGGATAATCTCAAAGAGTTTGATCAATTGGATCGA
GAGAATGATGATGGTTGGGCAGGGGCCCACGAAGAGATTGACTACACTGAAAAGCTCAAGTTCAGCGATGAGGAAGATGG
CCGAGACTCTGATGAGGAGGGAGCTGAGGGCCACAAGGATTCCCAGTCAGCTTCTGGTGAGGAACGGCCCCCTGAAGCAG
ATGGCAAAAAGGGCAACTCTCCCGGCACTGAACCGCCCCTCCTAAGACAGCCTGGGCAGAAACCTCTCAGCCTCCAGAGA
CAGACCCAGGACCTCCTGCCCCAAAGCCTCCCCCACCCCCACCTCACCGGGGCCCCGCCAGGAACTGGGGCCCCCCTGGG
GACTATCCAGATCGTGGGGGCCCTCCCTGCAAGCTCCCAGCACCTGAAGATGAGGATGAAGCATGGCGGCAGCGACGAAA
GCAGTCATCATCTGAGATTTCCCTGGCAGTGGAGCACACCCGACGACCGTGAGAAAAAGAGGAGCGGCACATGCAGGAAG
AGCGCCGGGCAGCCTGTGCTGAGAAGCTCAAGTGGCTTGATGAAAAGTTTGGGGCACCTGACAAGCGACTCAAAGCAGAG
CCTGCTCCCCCACCTGCTGCCCCTTCTACCCCAGCTCCACCACCTGCA

ORF - retro_cjac_572 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.98 %
Parental protein coverage: 95.26 %
Number of stop codons detected: 3
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMSDRSGPTAKGKDGKKYSSLNLFDTYKGKSLEIQKPAVAPRHGLQSLGKVAIARRMPPPANLPSLKAENK
MSDR.GPTAKG.DG.KYSSLNLFDTYKGKSLEIQKPAV.PRHGLQSL.KVAIARRMPPPANLPSLKAENK
RetrocopyMSDRWGPTAKGNDGNKYSSLNLFDTYKGKSLEIQKPAVVPRHGLQSLSKVAIARRMPPPANLPSLKAENK
ParentalGNDPNVSLVPKDGTGWASKQEQSDPKSSDASTAQPPESQPLPASQMPASNQPKRPPAAPENTPSVPSGVK
GNDPNVSLVPKDGTG.ASKQEQSDPKSSDASTAQPPESQPL.A...PASNQPKRPPAAPENTPSV.SGVK
RetrocopyGNDPNVSLVPKDGTG*ASKQEQSDPKSSDASTAQPPESQPLQAPPTPASNQPKRPPAAPENTPSVASGVK
ParentalSWAQASVTHGAHGDGGRASSLLSRFSREEFPTLQAAGDQDKAAKERESAEQSSGPGPSLRPQNSTTWRDG
SWAQ.SV..GAHGDGGRASSLLSRFSREEF.T.QAAG.Q.KAAKERESA..SSGPGPSL.PQNSTTWRDG
RetrocopySWAQVSVSYGAHGDGGRASSLLSRFSREEFLTQQAAGAQNKAAKERESAK*SSGPGPSLCPQNSTTWRDG
ParentalGGRGPDELEGPDSKLHHGHDPRGALQPSGPPQFPPYRGMMPPFMYPPYLPFPPPYGPQGPYRYPTPDGPS
GG.G.DELEGPDSKLHHGHDP.GALQPSGPPQFPPYRGMMPPFMYPPYLPFPPPYGPQGPYRYPTPDGPS
RetrocopyGGLGSDELEGPDSKLHHGHDPQGALQPSGPPQFPPYRGMMPPFMYPPYLPFPPPYGPQGPYRYPTPDGPS
ParentalRFPRVAGPRGSGPPMRLVEPVGRPSILKEDNLKEFDQLDQENDDGWAGAHEEVDYTEKLKFSDEEDGRDS
RFP.VAGPRGSGPP.RLVEPVG.PSILKEDNLKEFDQLD.ENDDGWAGAHEE.DYTEKLKFSDEEDGRDS
RetrocopyRFPHVAGPRGSGPPIRLVEPVGHPSILKEDNLKEFDQLDRENDDGWAGAHEEIDYTEKLKFSDEEDGRDS
ParentalDEEGAEGHKDSQSASGEERPPEADGKKGNSPGSEPP-PPKTAWAETSRPPETEPGPPAPKPPPPPPHRGP
DEEGAEGHKDSQSASGEERPPEADGKKGNSPG.EPP.PPKTAWAETS.PPET.PGPPAPKPPPPPPHRGP
RetrocopyDEEGAEGHKDSQSASGEERPPEADGKKGNSPGTEPP<PPKTAWAETSQPPETDPGPPAPKPPPPPPHRGP
ParentalAGNWGPPGDYPDRGGPPCKPPAPEDEDEAWRQRRKQSSSEISLAVERARRRREEEERRMQEERRAACAEK
A.NWGPPGDYPDRGGPPCK.PAPEDEDEAWRQRRKQSSSEISLAVE..RR..E.EER.MQEERRAACAEK
RetrocopyARNWGPPGDYPDRGGPPCKLPAPEDEDEAWRQRRKQSSSEISLAVEHTRRP*EKEERHMQEERRAACAEK
ParentalLKRLDEKFGAPDKRLKAEPAPPPAAPSTPAPPPA
LK.LDEKFGAPDKRLKAEPAPPPAAPSTPAPPPA
RetrocopyLKWLDEKFGAPDKRLKAEPAPPPAAPSTPAPPPA

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 .00 RPM 15 .29 RPM
SRP051959_heart 0 .02 RPM 29 .57 RPM
SRP051959_kidney 0 .00 RPM 18 .73 RPM
SRP051959_liver 0 .00 RPM 6 .28 RPM
SRP051959_lung 0 .03 RPM 19 .85 RPM
SRP051959_lymph_node 0 .00 RPM 22 .28 RPM
SRP051959_skeletal_muscle 0 .02 RPM 17 .19 RPM
SRP051959_spleen 0 .04 RPM 18 .30 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_572 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_572 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_572 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG00000003047 2 retrocopies
retro_cjac_571, retro_cjac_572 ,


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