RetrogeneDB ID:

retro_cjac_233

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:X:17917365..17918082(+)
Located in intron of:ENSCJAG00000005449
Retrocopy
information
Ensembl ID:ENSCJAG00000022320
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCJAG00000007167
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_233
ATAACCAAGCCATGTGGGGTGCACCTGAGCCGGGAGGTCCTCAAACAGGTAGAGGTCTTCAGGCAGAATCTTTTCCAGGA
GGCTGAGGAATTCCTCCACAGATTCTTGCCACAGAAAATCATATACCTGAATCAGCTCTTGCAAGAGGACTCCCTCAATG
TGGCTGACCTGACTTCCCTCCGAGCCACACTGGACATCCCCATCCCAGATCCTCCACCCAAGGATGATGAGATGGAAACA
GATAAGCAGAAGAAGAAAGAAATCCCTAAGTGTGGATTTCTCCCTGAGAATGAGGTCCTGTCCCTCCTTGCCCTGGTTAA
GTCAGAAGTCTGGACTCCCAAAGAGAAATGCATTCTGGTAATCACATGGATCCAGCACCTGATCCCCAAAATTGAAGACG
GAAATGATTTTGGGGTAGCAATCCAGGAAAAGGTACTGGAGAGGGTGAATGCCGTCAAGACCAAAGTGGAAGCTTTCCAG
ACAACCATTTCCAAGTACTTCTCAGAACATGGGGATGTTGTGGCCAAGGCCTCCAAGGAGACTCATGTGATGGATTACTG
GGCCTCAGTGCACGAGCGAGATGAGGCAGCCTATGGGGAGCTCAGGGCCATGGTGCTGGACCTGAAGGCCTTCTATGCTG
AGCTTTATCATATCATAAGCAGTAACCCGGAGAAAACTGTCAACCCAAAGGGTGAAGAGAAGCCATCTATGTACTGA

ORF - retro_cjac_233 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.21 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMAKPCGVRLSGEARKQVEVFRQNLFQEAEEFLYRFLPQKIIYLNQLLQEDSLNVADLTSLRATLDIPIPD
..KPCGV.LS.E..KQVEVFRQNLFQEAEEFL.RFLPQKIIYLNQLLQEDSLNVADLTSLRATLDIPIPD
RetrocopyITKPCGVHLSREVLKQVEVFRQNLFQEAEEFLHRFLPQKIIYLNQLLQEDSLNVADLTSLRATLDIPIPD
ParentalPPPKDDEMETDKQEKKEVPKCGFLPGNEKVLSLLALVKPEVWTLKEKCILLITWIQHLIPKIEDGNDFGV
PPPKDDEMETDKQ.KKE.PKCGFLP.NE.VLSLLALVK.EVWT.KEKCIL.ITWIQHLIPKIEDGNDFGV
RetrocopyPPPKDDEMETDKQKKKEIPKCGFLPENE-VLSLLALVKSEVWTPKEKCILVITWIQHLIPKIEDGNDFGV
ParentalAIQEKVLERVNAVKTKVEAFQTTISKYFSERGDAVAKASKETHVMDYRALVHERDEAAYGELRAMVLDLR
AIQEKVLERVNAVKTKVEAFQTTISKYFSE.GD.VAKASKETHVMDY.A.VHERDEAAYGELRAMVLDL.
RetrocopyAIQEKVLERVNAVKTKVEAFQTTISKYFSEHGDVVAKASKETHVMDYWASVHERDEAAYGELRAMVLDLK
ParentalAFYAELYHIISSNLEKIVNPKGEEKPSMY
AFYAELYHIISSN.EK.VNPKGEEKPSMY
RetrocopyAFYAELYHIISSNPEKTVNPKGEEKPSMY

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 .20 RPM 22 .41 RPM
SRP051959_heart 0 .28 RPM 11 .65 RPM
SRP051959_kidney 0 .20 RPM 22 .45 RPM
SRP051959_liver 0 .11 RPM 26 .30 RPM
SRP051959_lung 0 .70 RPM 21 .57 RPM
SRP051959_lymph_node 1 .05 RPM 37 .97 RPM
SRP051959_skeletal_muscle 0 .07 RPM 6 .51 RPM
SRP051959_spleen 0 .95 RPM 39 .83 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_233 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_233 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_233 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 13 parental genes, and 33 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG00000007167 3 retrocopies
retro_cjac_233 , retro_cjac_322, retro_cjac_71,
Callithrix jacchus ENSCJAG000000131111 retrocopy
Felis catus ENSFCAG000000055851 retrocopy
Homo sapiens ENSG000001009114 retrocopies
Gorilla gorilla ENSGGOG000000160254 retrocopies
Myotis lucifugus ENSMLUG000000097691 retrocopy
Macaca mulatta ENSMMUG000000124734 retrocopies
Mus musculus ENSMUSG000000791971 retrocopy
Nomascus leucogenys ENSNLEG000000152604 retrocopies
Otolemur garnettii ENSOGAG000000165841 retrocopy
Pongo abelii ENSPPYG000000056844 retrocopies
Pan troglodytes ENSPTRG000000061964 retrocopies
Sus scrofa ENSSSCG000000020041 retrocopy



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