RetrogeneDB ID:

retro_cjac_4066

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:X:53494061..53494994(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCJAG00000007345
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:FOXR1
Ensembl ID:ENSCJAG00000013656
Aliases:None
Description:forkhead box R1 [Source:HGNC Symbol;Acc:29980]


Retrocopy-Parental alignment summary:






>retro_cjac_4066
ATGGACTTAAAACTAAAAGATCTTGAATTTTGGTATAATCTCCAAGGCCAGGTACCAGGGCTGCTGGACTGGGACATGCA
GAATGAGTTATTTTTGTCTTGTACCACAGACCAGTGCTCCTTAACTGAGCAGCTCCTTAGCAAATATAGAATTCGAGTAA
TGAAGCCCCCAGAGATGCCTCAGAATAGGACACTCAGTCCTAATAAAGATGGTCCTCACTGTGAACCCAATCTGTGGATA
TGGGTGAACCCCAACATTCTGTGCCCCCTTGGCAGCCAGAAGGCCCCAAAGCCCATTGGAAAAAAGGATACGACAAGCAT
TTCTCCTTTCCCTCAGCCCTCACTAACAGATGAAGAGTCCAGCTGCTCAGAGGTCACAGTGGTAGAGTCCCTGTCATCTT
CCTCCAGTGAGCAGTCTCCTATACAGAAGCAAGATATCTATTCCCCTAACAACTTCGTGCTCACAGAAGAGGAGGCTGAG
AAACAAGAGGACAACTCCTTCCAGTCCTCTGAAAGGGAGTGCTTCCAGAGCCAGAAGCTATGGCAAATCAACAAGCAAGA
GAAGTCCTGGCAACGGATCCCTCTCAATTGTAGCCACCTTATTGCCCTAGCATTAAGAAAGAGCCCCCACTATGGCCTCA
GTGTGAAGGAGATCTACAGTTTCACCCAACACCATTTCCCCTTTTTCCGGACAGCTCCAGATGGCTGGAAGAGCACCATT
CATTATAACCTCTGCTTCCTGAGCAGCTTTGAGAAGGTACCAGACGACCTTCAGGGTGAAAATAATGCAAGATCTTGCTG
TTGCCGTTGGAGGCTCACTAAAGAGGGGCACCGCCGCTTTTTGGAGGAAACTCGTGCCTTAGCTGCTGCTCAAAGGGAGA
GCATCCAAGAGTGCATGAGTCAGCCAGACCTGTTTACCTCTCTCTTTGATCTT

ORF - retro_cjac_4066 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 53.77 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalVDVKLQHLDFWASLHGQVPGLLDWDMGNELFLAFTTSHLPLAEQKLARYKLRIVKPPKLPLEKKTNPDKD
.D.KL..L.FW..L.GQVPGLLDWDM.NELFL..TT....L.EQ.L..Y..R..KPP..P......P.KD
RetrocopyMDLKLKDLEFWYNLQGQVPGLLDWDMQNELFLSCTTDQCSLTEQLLSKYRIRVMKPPEMPQNRTLSPNKD
ParentalGPDYEPNLWMWVNPNIVYPPGKLEVPGLMKKEDLTSTLPSSQPFQKEEDASCSEPTGAESLSRSSSEWSP
GP..EPNLW.WVNPNI..P.G....P....K.D.TS..P..QP....E..SCSE.T..ESLS.SSSE.SP
RetrocopyGPHCEPNLWIWVNPNILCPLGSQKAPKPIGKKDTTSISPFPQPSLTDEESSCSEVTVVESLSSSSSEQSP
ParentalPQKRFAFSPSIWELTEEEEAEDQEDSSSVALPSPHKKAPLQSRRLRQASSQAGRLWSRPPLNYFHLIALA
.QK....SP....LTE....E..E........S.......QS..L.Q...Q....W.R.PLN..HLIALA
RetrocopyIQKQDIYSPNNFVLTE----EEAEKQEDNSFQSSEREC-FQSQKLWQINKQE-KSWQRIPLNCSHLIALA
ParentalLRNSSPCGLNVQQIYSFTRKHFPFFRTAPEGWKNTVRHNLCFRDSFEKVPVSSVQGGASARPRSCLWKLT
LR.S...GL.V..IYSFT..HFPFFRTAP.GWK.T...NLCF..SFEKVP....QG...AR...C.W.LT
RetrocopyLRKSPHYGLSVKEIYSFTQHHFPFFRTAPDGWKSTIHYNLCFLSSFEKVP-DDLQGENNARSCCCRWRLT
ParentalEEGHRRFEEEARALASTRLESIQRCMSQPDVMPFLFDL
.EGHRRF.EE.RALA....ESIQ.CMSQPD....LFDL
RetrocopyKEGHRRFLEETRALAAAQRESIQECMSQPDLFTSLFDL

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 0 .11 RPM
SRP051959_heart 0 .02 RPM 0 .14 RPM
SRP051959_kidney 0 .00 RPM 0 .07 RPM
SRP051959_liver 0 .00 RPM 0 .17 RPM
SRP051959_lung 0 .02 RPM 0 .28 RPM
SRP051959_lymph_node 0 .00 RPM 0 .39 RPM
SRP051959_skeletal_muscle 0 .00 RPM 0 .02 RPM
SRP051959_spleen 0 .02 RPM 0 .25 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_4066 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_4066 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_4066 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_72
Pan troglodytes retro_ptro_94
Pongo abelii retro_pabe_69
Bos taurus retro_btau_189
Parental genes homology:
Parental genes homology involve 18 parental genes, and 18 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000000531 retrocopy
retro_amel_39,
Bos taurus ENSBTAG000000146061 retrocopy
retro_btau_189,
Canis familiaris ENSCAFG000000124171 retrocopy
retro_cfam_209,
Callithrix jacchus ENSCJAG00000013656 1 retrocopy
retro_cjac_4066 ,
Dasypus novemcinctus ENSDNOG000000094141 retrocopy
retro_dnov_22,
Dipodomys ordii ENSDORG000000019601 retrocopy
retro_dord_651,
Homo sapiens ENSG000001763021 retrocopy
retro_hsap_72,
Microcebus murinus ENSMICG000000026801 retrocopy
retro_mmur_38,
Macaca mulatta ENSMMUG000000227221 retrocopy
retro_mmul_125,
Mustela putorius furoENSMPUG000000048901 retrocopy
retro_mputfur_161,
Nomascus leucogenys ENSNLEG000000073761 retrocopy
retro_nleu_50,
Otolemur garnettii ENSOGAG000000072581 retrocopy
retro_ogar_296,
Procavia capensis ENSPCAG000000101321 retrocopy
retro_pcap_12,
Pongo abelii ENSPPYG000000039471 retrocopy
retro_pabe_69,
Pan troglodytes ENSPTRG000000043581 retrocopy
retro_ptro_94,
Sorex araneus ENSSARG000000113191 retrocopy
retro_sara_38,
Sus scrofa ENSSSCG000000151011 retrocopy
retro_sscr_36,
Ictidomys tridecemlineatus ENSSTOG000000143211 retrocopy
retro_itri_158,


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