RetrogeneDB ID:

retro_cjac_543

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:1:71046589..71047979(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PAPOLA
Ensembl ID:ENSCJAG00000006512
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_543
ATTACAACACAGGGATCACAACAAACACAACCACCACACAAGCACTATGGCATCACTTCTCCTATCAGCTTAGCAGCCCC
CAAGGAGACTAACTGCATACTTACACAGAAACTAATTGAGACACTGAAACCCTTCAGGGTTTTTGATGAGGAAGAGGAAC
TGCAGCGCAGGATTCTAATTTTGGGAAAACTAACCTGGTAAAAAAGTGGATACGAGAAATCAATGAAAGCAAGAATCTTC
AATTACAGTCTGTAATTGAAAATATTGGAGGACAAATTTTTACATTTGGATCTTACGGTTAGGCGTACATACAGAAGGTG
CTGAATTGGATGCGTTGTGTGTTGCACCAAGACATGTTGATCGAGGTGACTTTTTCACCTCATTCTATGATGAGTTGAAA
TTACAGGAAGAAGTAAAAGATTTAAGAGCTGTTGAAGAGGCATTCATACCAGTTATTAAACTCTGTTTTGATGGGATAGA
GATGGATATTTTGTTTGCAAGATTAGCACTGCCGACAATTCCAGAAGATTTGGACCTACGAGATGACAGTCTGCTTAAAA
ATTTAGATATAAGATGTATTAAGAAGTCTTAACGGTTGCAGGGTAACCGATGAAATTTTACATCTAGTACCAAACATTGA
CAACTTCAGGTTAACTATGAGAGCTAACAAACTGTGGGCCAAACGCCACAACATCTATTCCAATATATTAGGTTTCCTCA
GTGGTGTTTCCTGGGCTATGCTAGTAGCAAGAACTTGCCAGCTTTATCCAAATGCAATAGCATCAACACTTGTACATAAA
TTTTTCTTGGTATTTTCTAAATGGGAATGGCCAAATCCCGTGCTATTGAAACAGCCTGAAGAATGCAATCTTAATTTGCC
TGTATGGGACCCAAGGGTAAATCCCAGTGATAGGTACCATCTTATGCCTATAATTACACCAGCATACCGACAACAGAACT
CCACAGTACAACGTGTTCGTTTCAACATGGGTGGTCATGGTTGAGGAGTTTAAACGGGTTTTGCTATCACAGATGAAATT
TTGCTGAGTAAGGCAGAGTGGTCTAAACTTTTTGAAGCTCCAAACTTCTTTCAAAAGTACAGGCATTATATTGTACTTCT
AGCAAGTGCACCAACAGAAAAACAACACCTAGAATGGGCGGGCTTGGTGGAATCAAGAATCTGAATCCTAGTTGGAAGCT
TGGAGAAGATTGAATTTATTACACTGGTGCATGTGAATCCCCAGTCATTTCCAGCACCCAAAGAAAATCCTGACAAGGAA
GAATTTCACACGATGTGGGTGATTGGGTCAGTGTTTAAAAAACAGAAAACTCTGAAAACCTCAGTTTTGATCTCACCTAT
GATATTCAGTCTTTCACAGATACAGTTTTT

ORF - retro_cjac_543 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.02 %
Parental protein coverage: 72.73 %
Number of stop codons detected: 1
Number of frameshifts detected 6


Retrocopy - Parental Gene Alignment:

ParentalVTTQGSQQTQPPQKHYGITSPISLAAPKETDCILTQKLIETLKPFGVFEEEEELQRRILIL-GKLNNLVK
.TTQGSQQTQPP.KHYGITSPISLAAPKET.CILTQKLIETLKPF.VF.EEEELQRRILIL.GK..NLVK
RetrocopyITTQGSQQTQPPHKHYGITSPISLAAPKETNCILTQKLIETLKPFRVFDEEEELQRRILIL<GK-TNLVK
ParentalEWIREISESKNLP-QSVIENVGGKIFTFGSY-RLGVHTKGADIDALCVAPRHVDRSDFFTSFYDKLKLQE
.WIREI.ESKNL..QSVIEN.GG.IFTFGSY.RLGVHT.GA..DALCVAPRHVDR.DFFTSFYD.LKLQE
RetrocopyKWIREINESKNLQLQSVIENIGGQIFTFGSY<RLGVHTEGAELDALCVAPRHVDRGDFFTSFYDELKLQE
ParentalEVKDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRCI-RSLNGCRVTDEI
EVKDLRAVEEAF.PVIKLCFDGIE.DILFARLAL.TIPEDLDLRDDSLLKNLDIRCI.RSLNGCRVTDEI
RetrocopyEVKDLRAVEEAFIPVIKLCFDGIEMDILFARLALPTIPEDLDLRDDSLLKNLDIRCI>RSLNGCRVTDEI
ParentalLHLVPNIDNFRLTLRAIKLWAKRHNIYSNILGFLGGVSWAMLVARTCQLYPNAIASTLVHKFFLVFSKWE
LHLVPNIDNFRLT.RA.KLWAKRHNIYSNILGFL.GVSWAMLVARTCQLYPNAIASTLVHKFFLVFSKWE
RetrocopyLHLVPNIDNFRLTMRANKLWAKRHNIYSNILGFLSGVSWAMLVARTCQLYPNAIASTLVHKFFLVFSKWE
ParentalWPNPVLLKQPEECNLNLPVWDPRVNPSDRYHLMPIITPAYPQQNST-YNVSVSTRMVMVEEFKQ-GLAIT
WPNPVLLKQPEECNLNLPVWDPRVNPSDRYHLMPIITPAY.QQNST.YNV.VST..VMVEEFK..G.AIT
RetrocopyWPNPVLLKQPEECNLNLPVWDPRVNPSDRYHLMPIITPAYRQQNST>YNVFVSTWVVMVEEFKR<GFAIT
ParentalDEILLSKAEWSKLFEAPNFFQKYKHYIVLLASAPTEKQRLEWVGLVESKIRILVGSLEKNEFITLAHVNP
DEILLSKAEWSKLFEAPNFFQKY.HYIVLLASAPTEKQ.LEW.GLVES.I.ILVGSLEK.EFITL.HVNP
RetrocopyDEILLSKAEWSKLFEAPNFFQKYRHYIVLLASAPTEKQHLEWAGLVESRI*ILVGSLEKIEFITLVHVNP
ParentalQSFPAPKENPDKEEFRTMWVIGLVFK-KTENSENLSVDLTYDIQSFTDTVY
QSFPAPKENPDKEEF.TMWVIG.VFK.KTENSENLS.DLTYDIQSFTDTV.
RetrocopyQSFPAPKENPDKEEFHTMWVIGSVFK<KTENSENLSFDLTYDIQSFTDTVF

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 99 .18 RPM
SRP051959_heart 0 .02 RPM 79 .07 RPM
SRP051959_kidney 0 .07 RPM 99 .35 RPM
SRP051959_liver 0 .02 RPM 87 .49 RPM
SRP051959_lung 0 .07 RPM 113 .47 RPM
SRP051959_lymph_node 0 .09 RPM 137 .71 RPM
SRP051959_skeletal_muscle 0 .04 RPM 58 .79 RPM
SRP051959_spleen 0 .00 RPM 114 .77 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_543 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_543 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_543 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 17 parental genes, and 19 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000141421 retrocopy
retro_amel_517,
Bos taurus ENSBTAG000000040541 retrocopy
retro_btau_1078,
Canis familiaris ENSCAFG000000177831 retrocopy
retro_cfam_1783,
Callithrix jacchus ENSCJAG00000006512 2 retrocopies
retro_cjac_1763, retro_cjac_543 ,
Homo sapiens ENSG000000900601 retrocopy
retro_hsap_30,
Gorilla gorilla ENSGGOG000000062871 retrocopy
retro_ggor_202,
Myotis lucifugus ENSMLUG000000109221 retrocopy
retro_mluc_1396,
Macaca mulatta ENSMMUG000000186101 retrocopy
retro_mmul_1675,
Monodelphis domestica ENSMODG000000128872 retrocopies
retro_mdom_1714, retro_mdom_1916,
Mustela putorius furoENSMPUG000000030541 retrocopy
retro_mputfur_1375,
Mus musculus ENSMUSG000000211111 retrocopy
retro_mmus_37,
Nomascus leucogenys ENSNLEG000000006251 retrocopy
retro_nleu_2771,
Otolemur garnettii ENSOGAG000000046111 retrocopy
retro_ogar_987,
Pongo abelii ENSPPYG000000061281 retrocopy
retro_pabe_3113,
Pan troglodytes ENSPTRG000000067041 retrocopy
retro_ptro_2595,
Pteropus vampyrus ENSPVAG000000139251 retrocopy
retro_pvam_360,
Vicugna pacos ENSVPAG000000064641 retrocopy
retro_vpac_378,


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