RetrogeneDB ID:

retro_cjac_272

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:1:54742098..54742833(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCJAG00000023309
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCJAG00000021032
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_272
TGTTGCACAGACTCTGGAACCATGAACATATTTGATCGAAAGATCAACTTTGATGTGCTTTTAAAATTTTCTCATATAAC
CCCCTCAACACAGCAGCACCTGAAGAAGGTCTACGCAAGTTTTGCCCTTTATATGTTTGTGGCGGCTGCGGGGGCCTATG
TCCATGTGATCACTCATTTCATTCAGGCTGGCCTGCTGTCTGCTTTGGGCTCCCTGATATTGATGATTTGGCTGATGGCA
ACACCTCACAGCCATGAAACTGAGCAAAAAAGACTGGGACTTCTTGCTGGATTTGCTTTCCTTACAGGAGTTGTCCTGGG
CCCTGCCCTGGAGTTTTGCATTGCCATCAACCCCAGCATCCTTCCCACCGCTTTCATGGGCACAGCAATGATCTTCACCT
GCTTTACCCTGAGTGCACTCTATGCCAAGCGTCGTAGCTACCTCTTTCTGGGAGGTATCTTGATGTCAGCCCTGAGCCTA
TTGCTTTTGTCTTCCCTGGGGAATGTTTTCTTTGGATCCATTTGGCTTTTCCAAGCAAACCTATATGTGGGACTGGTGGT
CATGTGTGGCTTTGTCCTTTTTGATACTCAACTCATTATTGAAAAGGCTGAAAATGGAGATCAAGATTATATCTGGCACT
GCATTGATCTCTTCTTAGATTTCATTACTCTCTTCAGAAAACTCACGATGATCCTGGCCATGAACGAAAAGGATAAGAAG
AAAGAGAAGAAATGA

ORF - retro_cjac_272 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 97.89 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMNIFDRKINFDALLKFSHITPSTQQHLKKVYASFALCMFVAAAGAYVHVITHFIQAGLLSALGSLILMIW
MNIFDRKINFD.LLKFSHITPSTQQHLKKVYASFAL.MFVAAAGAYVHVITHFIQAGLLSALGSLILMIW
RetrocopyMNIFDRKINFDVLLKFSHITPSTQQHLKKVYASFALYMFVAAAGAYVHVITHFIQAGLLSALGSLILMIW
ParentalLMATPHSHETEQKRLGLLAGFAFLTGVGLGPALEFCIAINPSILPTAFMGTAMIFTCFTLSALYAKRRSY
LMATPHSHETEQKRLGLLAGFAFLTGV.LGPALEFCIAINPSILPTAFMGTAMIFTCFTLSALYAKRRSY
RetrocopyLMATPHSHETEQKRLGLLAGFAFLTGVVLGPALEFCIAINPSILPTAFMGTAMIFTCFTLSALYAKRRSY
ParentalLFLGGILMSALSLLLLSSLGNVFFGSIWLFQANLYVGLVVMCGFVLFDTQLIIEKAENGDQDYIWHCIDL
LFLGGILMSALSLLLLSSLGNVFFGSIWLFQANLYVGLVVMCGFVLFDTQLIIEKAENGDQDYIWHCIDL
RetrocopyLFLGGILMSALSLLLLSSLGNVFFGSIWLFQANLYVGLVVMCGFVLFDTQLIIEKAENGDQDYIWHCIDL
ParentalFLDFITLFRKLMMILALNEKDKKKEKK
FLDFITLFRKL.MILA.NEKDKKKEKK
RetrocopyFLDFITLFRKLTMILAMNEKDKKKEKK

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 2 .04 RPM 123 .81 RPM
SRP051959_heart 0 .54 RPM 46 .69 RPM
SRP051959_kidney 5 .59 RPM 328 .24 RPM
SRP051959_liver 7 .95 RPM 432 .02 RPM
SRP051959_lung 2 .16 RPM 103 .31 RPM
SRP051959_lymph_node 1 .58 RPM 71 .46 RPM
SRP051959_skeletal_muscle 1 .16 RPM 61 .98 RPM
SRP051959_spleen 0 .86 RPM 92 .00 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_272 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_272 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_272 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 11 parental genes, and 19 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000185881 retrocopy
Canis familiaris ENSCAFG000000084002 retrocopies
Callithrix jacchus ENSCJAG00000021032 1 retrocopy
retro_cjac_272 ,
Dasypus novemcinctus ENSDNOG000000078822 retrocopies
Macropus eugenii ENSMEUG000000155904 retrocopies
Monodelphis domestica ENSMODG000000042772 retrocopies
Otolemur garnettii ENSOGAG000000051372 retrocopies
Pteropus vampyrus ENSPVAG000000168211 retrocopy
Sarcophilus harrisii ENSSHAG000000103661 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000011652 retrocopies
Tarsius syrichta ENSTSYG000000024271 retrocopy



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