RetrogeneDB ID:

retro_cjac_64

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:20:44013301..44013892(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCJAG00000038002
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCJAG00000008520
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_64
ATGAGTATGCTCAGGCTTCAGAAGAGGCTCGCCTCTAGTGTCCTCCGCTGTGGCAAGAAGAAGGTCTGGTTGGACCCGAA
TGAGACCAATGAAATCGCCAATGCTAACTCGCGTCAGCAGATCCGGAAGCTGATCAAAGATGGGCTGATCATCCGAAAGC
CTGTGACGGTCCATTCCCGGGCTCGCTGCCGGAAAAACACCTTGGCCCGCCGGAAGGGCAGGCACATGGGCATAGGTAAG
CATAAGGGTACAGCCAATGCCCGAATGCCAGAGAAGGTCATGTGGATGAGAAGAATGAGGATTCTGCACCGGCTGCTCAG
AAGATACCGGGAATCTAAGAAAATTGATCGCCACATGTATCACAGCCTGTACCTGAAGGTGAAGGGGAATGTGTTCAAAA
ACAAGCGGATTCTCATGGAACACATCCACAAGCTGAAGGCAGACAAGGCCCGCAAGAAGCTCCTGGCTGACCAGGCTGAG
GCCCGCAGGTCTAAGACCAAGGAAGCACGAAAGCGCCGTGAAGAACGCCTCCAGGCCAAAAAGGAGGAGATCATCAAAAC
TTTGTCCAAGGAGGAAGAGACCAAGAAATAA

ORF - retro_cjac_64 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 98.47 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMSMLRLQKRLASSVLRCGKKKVWLDPNETNEIANANSRQQIRKLIKDGLIIRKPVTVHSRARCRKNTLAR
MSMLRLQKRLASSVLRCGKKKVWLDPNETNEIANANSRQQIRKLIKDGLIIRKPVTVHSRARCRKNTLAR
RetrocopyMSMLRLQKRLASSVLRCGKKKVWLDPNETNEIANANSRQQIRKLIKDGLIIRKPVTVHSRARCRKNTLAR
ParentalRKGRHMGIGKRKGTANARMPEKVTWMRRMRILRRLLRRYRESKKIDRHMYHSLYLKVKGNVFKNKRILME
RKGRHMGIGK.KGTANARMPEKV.WMRRMRIL.RLLRRYRESKKIDRHMYHSLYLKVKGNVFKNKRILME
RetrocopyRKGRHMGIGKHKGTANARMPEKVMWMRRMRILHRLLRRYRESKKIDRHMYHSLYLKVKGNVFKNKRILME
ParentalHIHKLKADKARKKLLADQAEARRSKTKEARKRREERLQAKKEEIIKTLSKEEETKK
HIHKLKADKARKKLLADQAEARRSKTKEARKRREERLQAKKEEIIKTLSKEEETKK
RetrocopyHIHKLKADKARKKLLADQAEARRSKTKEARKRREERLQAKKEEIIKTLSKEEETKK

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 .07 RPM 109 .65 RPM
SRP051959_heart 0 .09 RPM 116 .94 RPM
SRP051959_kidney 0 .18 RPM 133 .96 RPM
SRP051959_liver 0 .19 RPM 160 .44 RPM
SRP051959_lung 0 .03 RPM 153 .06 RPM
SRP051959_lymph_node 0 .14 RPM 248 .99 RPM
SRP051959_skeletal_muscle 0 .09 RPM 157 .36 RPM
SRP051959_spleen 0 .17 RPM 213 .30 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_64 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_64 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_64 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 30 parental genes, and 300 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000041215 retrocopies
Bos taurus ENSBTAG000000020605 retrocopies
Canis familiaris ENSCAFG0000001649314 retrocopies
Choloepus hoffmanni ENSCHOG000000060237 retrocopies
Callithrix jacchus ENSCJAG00000008520 4 retrocopies
Dasypus novemcinctus ENSDNOG000000197427 retrocopies
Dipodomys ordii ENSDORG000000043301 retrocopy
Equus caballus ENSECAG000000250806 retrocopies
Homo sapiens ENSG0000010829821 retrocopies
Loxodonta africana ENSLAFG000000182573 retrocopies
Macropus eugenii ENSMEUG0000001390010 retrocopies
Microcebus murinus ENSMICG000000026635 retrocopies
Myotis lucifugus ENSMLUG0000001255511 retrocopies
Macaca mulatta ENSMMUG000000042352 retrocopies
Monodelphis domestica ENSMODG000000126932 retrocopies
Mustela putorius furoENSMPUG000000150415 retrocopies
Mus musculus ENSMUSG0000001740425 retrocopies
Nomascus leucogenys ENSNLEG0000000074819 retrocopies
Ochotona princeps ENSOPRG000000070922 retrocopies
Procavia capensis ENSPCAG000000152281 retrocopy
Pongo abelii ENSPPYG0000000849220 retrocopies
Pan troglodytes ENSPTRG0000000908622 retrocopies
Pteropus vampyrus ENSPVAG000000084989 retrocopies
Rattus norvegicus ENSRNOG0000000474137 retrocopies
Sarcophilus harrisii ENSSHAG000000164824 retrocopies
Sus scrofa ENSSSCG000000175093 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000111205 retrocopies
Tupaia belangeri ENSTBEG0000000807731 retrocopies
Tarsius syrichta ENSTSYG0000000869810 retrocopies
Tursiops truncatus ENSTTRG000000066874 retrocopies



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