RetrogeneDB ID:

retro_cjac_210

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:6:347351..348875(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCJAG00000022162
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:MKRN1
Ensembl ID:ENSCJAG00000013474
Aliases:None
Description:makorin ring finger protein 1 [Source:HGNC Symbol;Acc:7112]


Retrocopy-Parental alignment summary:






>retro_cjac_210
ATGGAAGAGCCTGCAGCTCCCTCAGAAGCCCACGAGGCAGCCGGGGCCCAGGCAGGTGCTGAGGCAGCAGGGGAGGGTGT
GTCTGGGCCCGACCTTCCCGCGTGTGAGCCCTCCGGGGAATCTGCTGCTCCAGATTCAGCACTGCCACATGTGGCCGTGG
GCTGGGCCCCCTTCCCTGTAGCTCCAGTCCCTGCCCACCTCCGCACGGGAGGCCTGAGGCCTGCCCCAGCCTCCGGAGGA
GGAGCCTGGCCCAGCCCCTTGCCAAGCCGAAGCAGTGGCATTTGGACAAAGCAGATCGCCTGCAGGTATTATATACATGG
GCAGTGCAAGGAGGGGGAGAACTGTCGCTATTCCCACGACCTTTCTTGTCGGAAGATGGCCACCGAGGGCCGCGTTTCGC
CGTCTGGGGCCTCTGCAAGTGGAGGCCCTAGCACGGCTGCGCACATCGAGCCCCCGACTCAGGAAGTGGCGGAAGCCCCC
CCGGCTGCATCCTCGCAGTCCTTGCCTGTGATTGGCTCGGCTGCTGAAAGGGGTTTCTTTGAAGCCGAGAGAGACAATGC
AGACCGTGGAGCTGCTGGAGAAGCAGGTGTAGAAAGCTGGGCGGATGCCATTGAGTTTGTTCCAGGGCAGCCCTACCGGG
GCCGCCGGGTTGCATCTGCTCCTGAGGCTCCTCTACAGAGCTCAGAGACTGAGAGGAAGCAGATGGCTGTGGGCAGGGGT
GAGCGGTTTTGCTATTATGCTTCCAGGGGAGTTTGCTTTCGTGGGGAGAGCTGTATGTACCTCCATGGAGACATATGCGA
CATGTGTGGGCTGCAGGCCTTGCACCCCATGGATGCTGCCCAAAGGGAAGACCATATAAGGGCCTGCATTGAAGCACACG
AGAAAGATATGGAACTCTCGTTTGCTGTGCAGCGTGGTATGGACAAGGTGTGTGGCATCTGCATGGAGGTTGTCTATGAG
AAAGCCAACCCCAATGACCGCCGATTTGGCATTCTTTCCAATTGCAACCATACCTTCTGTATTAGGTGTATCCGCAGGTG
GAGAAGTGCCAGACAGTTTGATAACAGGATCATCAAGTCTTGTCCACAGTGCAGGGTCACCTCCGACTTGGTCATTCCCA
GTGAGTTCTGGGTGGAGGAGGAGGAAGAGAAGCAGAAACTTATTCAGCAATACAAAGAGGCAATGAGCAACAAGGCCTGC
AGGTATTTTGCGGAAGGCAGGGGTAACTGCCCATTTGGAGACACATGCTTTTACAAGCATGAATACCCTGAGGGCTGGGG
AGATGAGCCTCCTGGGCCGGGTGGTGGGTCATTCAGTGCATACTGGCATCAACTTGTGGAGCCTGTGCGAATGGGAGAGG
GCAACGCGCTCTATAAAAGCAGTAAGAAGGAGCTTGTCGTGCTTCGGCTGGCCAGTCTGTTGTTTAAGCAGTTTCTTTCA
CTGAGAGATGAGTTCCCCTTCTCTGAGGAGCAGTGGGACTTGCTTCATTATGAGCTGGAAGAATATTTCAATTTGAATCT
GTAG

ORF - retro_cjac_210 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 62.8 %
Parental protein coverage: 77.25 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalTELTTKSSLATSSSLSSVVGPLVEMNTSDAESRNSNFATVG-AGSEDWVNAIEFVPGQPYCGRTAPSCTE
T........A.SS....V.G...E.....AE..N......G.AG.E.W..AIEFVPGQPY.GR...S..E
RetrocopyTQEVAEAPPAASSQSLPVIGSAAERGFFEAERDNADRGAAGEAGVESWADAIEFVPGQPYRGRRVASAPE
ParentalAPLQGSVTKEESEKEQTTVETKKQLCPYAAVGECRYGENCVYLHGDSCDMCGLQVLHPMDAAQRSEHIKS
APLQ.S....E.E..Q..V......C.YA..G.C..GE.C.YLHGD.CDMCGLQ.LHPMDAAQR..HI..
RetrocopyAPLQSS----ETERKQMAVGRGERFCYYASRGVCFRGESCMYLHGDICDMCGLQALHPMDAAQREDHIRA
ParentalCIEAHEKDMELSFAVQRSKDMVCGICMEVVYEKANPSERRFGILSNCNHTYCLKCIRKWRSAKQFESKII
CIEAHEKDMELSFAVQR..D.VCGICMEVVYEKANP..RRFGILSNCNHT.C..CIR.WRSA.QF...II
RetrocopyCIEAHEKDMELSFAVQRGMDKVCGICMEVVYEKANPNDRRFGILSNCNHTFCIRCIRRWRSARQFDNRII
ParentalKSCPECRITSNFVIPSEYWVEEKEEKQKLILKYKEAMSNKACRYFDEGRGSCPFGGNCFYKHAYPDGRRE
KSCP.CR.TS..VIPSE.WVEE.EEKQKLI..YKEAMSNKACRYF.EGRG.CPFG..CFYKH.YP.G...
RetrocopyKSCPQCRVTSDLVIPSEFWVEEEEEKQKLIQQYKEAMSNKACRYFAEGRGNCPFGDTCFYKHEYPEGWGD
ParentalEPQRQKVGTSSRY
EP.....G..S.Y
RetrocopyEPPGPGGGSFSAY

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 .04 RPM 35 .41 RPM
SRP051959_heart 0 .09 RPM 25 .40 RPM
SRP051959_kidney 0 .00 RPM 45 .59 RPM
SRP051959_liver 0 .02 RPM 25 .00 RPM
SRP051959_lung 0 .20 RPM 42 .44 RPM
SRP051959_lymph_node 0 .05 RPM 27 .26 RPM
SRP051959_skeletal_muscle 0 .00 RPM 31 .14 RPM
SRP051959_spleen 0 .21 RPM 35 .92 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_210 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_210 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_210 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 25 parental genes, and 54 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000083062 retrocopies
retro_btau_401, retro_btau_943,
Canis familiaris ENSCAFG000000039532 retrocopies
retro_cfam_2157, retro_cfam_253,
Choloepus hoffmanni ENSCHOG000000110153 retrocopies
retro_chof_173, retro_chof_2357, retro_chof_89,
Callithrix jacchus ENSCJAG00000013474 2 retrocopies
retro_cjac_210 , retro_cjac_2991,
Callithrix jacchus ENSCJAG000000167331 retrocopy
retro_cjac_2362,
Cavia porcellus ENSCPOG000000009481 retrocopy
retro_cpor_109,
Dasypus novemcinctus ENSDNOG000000195642 retrocopies
retro_dnov_1011, retro_dnov_388,
Erinaceus europaeus ENSEEUG000000011331 retrocopy
retro_eeur_643,
Felis catus ENSFCAG000000249421 retrocopy
retro_fcat_67,
Homo sapiens ENSG000001336064 retrocopies
retro_hsap_1140, retro_hsap_4197, retro_hsap_4676, retro_hsap_4859,
Gorilla gorilla ENSGGOG000000239774 retrocopies
retro_ggor_119, retro_ggor_2813, retro_ggor_3031, retro_ggor_381,
Macropus eugenii ENSMEUG000000073991 retrocopy
retro_meug_1659,
Microcebus murinus ENSMICG000000021141 retrocopy
retro_mmur_1184,
Macaca mulatta ENSMMUG000000104203 retrocopies
retro_mmul_191, retro_mmul_2597, retro_mmul_76,
Mus musculus ENSMUSG000000299221 retrocopy
retro_mmus_2663,
Nomascus leucogenys ENSNLEG000000019214 retrocopies
retro_nleu_1027, retro_nleu_2167, retro_nleu_33, retro_nleu_939,
Otolemur garnettii ENSOGAG000000098772 retrocopies
retro_ogar_3468, retro_ogar_424,
Ochotona princeps ENSOPRG000000103531 retrocopy
retro_opri_1073,
Procavia capensis ENSPCAG000000146831 retrocopy
retro_pcap_19,
Pongo abelii ENSPPYG000000180573 retrocopies
retro_pabe_3435, retro_pabe_3776, retro_pabe_947,
Pan troglodytes ENSPTRG000000197665 retrocopies
retro_ptro_2849, retro_ptro_3106, retro_ptro_3234, retro_ptro_75, retro_ptro_776,
Sus scrofa ENSSSCG000000164982 retrocopies
retro_sscr_43, retro_sscr_637,
Tupaia belangeri ENSTBEG000000045642 retrocopies
retro_tbel_1410, retro_tbel_71,
Tarsius syrichta ENSTSYG000000099963 retrocopies
retro_tsyr_1256, retro_tsyr_1525, retro_tsyr_508,
Tursiops truncatus ENSTTRG000000095282 retrocopies
retro_ttru_1064, retro_ttru_1128,


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