RetrogeneDB ID:

retro_cjac_219

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:7:96092671..96093436(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCJAG00000022998
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCJAG00000014547
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_219
ATGAGTCGTCGCTGGGCTTGGCGGTTCTTGCTTTTCCAAGGCAGCGGAGATCGCTGGGTTTCAAGCCCCCGCGGGCATTT
CTCGCCGGCCCTGCGGAGAGACTTCTTCACTATCACAACCAAAGAGGGATATGATAGGCGTCCAGTGGACATAACTCCTT
TAGAACAAAGGAAATTAACTTTTGATACCCATGCATTGGTTCAGGACTTGGAAACTCATGGATTTGACAAAACACAAGCA
GAAACAATTGTATCAGCATTAACTACTTTATCAAATGTCAGCCTGGATACTATCTATAAAGAGATGATCACTCAAGCTCA
ACAGGAAATAACAGTACAACAGCTAATGGCTCATTTGGACTCTATCAGGAAAGACATGGTCATCCTAGAGAAAAGTGAAT
TTGCAAATCTGAGAGCTGAGAATGAGAAAATGAAAATTGAACTAGACCAAGTTAAGCAACAACTAATGCATGAAACCAGT
CGAATCAGAGCAGATAATAAACTGGGTATCAACCTAGAAAGGAGCAGAGTAACAGATATGTTTACAGATCAAGAAAAGCA
ACTTATGGAAGCAACTACAGAATTTACAAAAAAAGATACCCAAACCAAAAGTATTATTTCAGAGACCAGTAATAAAATTG
ATGCTGAAATTGCTTCCTTAAAAACACTGATGGAGTCTAACAAACTTGAGACCATTCGTTATCTTGCAGCCTCAGTGTTT
ACTTGCCTGGCAATAGCATTGGGATTTTATAGATTCTGGAAGTAG

ORF - retro_cjac_219 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 98.03 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMSRRRAWRFLLFQGSGDRWVSSPRGHFSPALRRGFFTTTTKEGYDRRPVDITPLEQRKLTFDTHALVQDL
MSRR.AWRFLLFQGSGDRWVSSPRGHFSPALRR.FFT.TTKEGYDRRPVDITPLEQRKLTFDTHALVQDL
RetrocopyMSRRWAWRFLLFQGSGDRWVSSPRGHFSPALRRDFFTITTKEGYDRRPVDITPLEQRKLTFDTHALVQDL
ParentalETHGFDKTQAETIVSALTTLSNVSLDTIYKEMVTQAQQEITVQQLMAHLDSIRKDMVILEKSEFANLRAE
ETHGFDKTQAETIVSALTTLSNVSLDTIYKEM.TQAQQEITVQQLMAHLDSIRKDMVILEKSEFANLRAE
RetrocopyETHGFDKTQAETIVSALTTLSNVSLDTIYKEMITQAQQEITVQQLMAHLDSIRKDMVILEKSEFANLRAE
ParentalNEKMKIELDQVKQQLMHETSRIRADNKLDINLERSRVTDMFTDQEKQLMEATTEFTKKDTQTKSIISETS
NEKMKIELDQVKQQLMHETSRIRADNKL.INLERSRVTDMFTDQEKQLMEATTEFTKKDTQTKSIISETS
RetrocopyNEKMKIELDQVKQQLMHETSRIRADNKLGINLERSRVTDMFTDQEKQLMEATTEFTKKDTQTKSIISETS
ParentalNKIDAEIASLKTLMESNKLETIRYLAASVFTCLAIALGFYRFWK
NKIDAEIASLKTLMESNKLETIRYLAASVFTCLAIALGFYRFWK
RetrocopyNKIDAEIASLKTLMESNKLETIRYLAASVFTCLAIALGFYRFWK

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 .16 RPM 4 .13 RPM
SRP051959_heart 0 .25 RPM 6 .52 RPM
SRP051959_kidney 0 .47 RPM 6 .74 RPM
SRP051959_liver 0 .26 RPM 5 .52 RPM
SRP051959_lung 0 .33 RPM 6 .28 RPM
SRP051959_lymph_node 0 .27 RPM 5 .00 RPM
SRP051959_skeletal_muscle 0 .35 RPM 5 .39 RPM
SRP051959_spleen 0 .29 RPM 6 .11 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_219 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_219 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_219 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 15 parental genes, and 19 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000105412 retrocopies
Callithrix jacchus ENSCJAG00000014547 1 retrocopy
retro_cjac_219 ,
Callithrix jacchus ENSCJAG000000160501 retrocopy
Homo sapiens ENSG000001375001 retrocopy
Macaca mulatta ENSMMUG000000201542 retrocopies
Nomascus leucogenys ENSNLEG000000164781 retrocopy
Ochotona princeps ENSOPRG000000041442 retrocopies
Pongo abelii ENSPPYG000000037361 retrocopy
Pan troglodytes ENSPTRG000000041291 retrocopy
Pteropus vampyrus ENSPVAG000000054591 retrocopy
Rattus norvegicus ENSRNOG000000094621 retrocopy
Tupaia belangeri ENSTBEG000000146652 retrocopies
Tarsius syrichta ENSTSYG000000111961 retrocopy
Tursiops truncatus ENSTTRG000000039981 retrocopy
Vicugna pacos ENSVPAG000000077531 retrocopy



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