RetrogeneDB ID:

retro_cjac_78

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:4:82755965..82756760(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCJAG00000023076
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCJAG00000002268
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_78
ATGGCGGTTGGCAAGAACAAGCGCCTTACGAAAGGCGGTAAAAAGGGAGCCAAGAAGAAAGTGGTTGATCCATTTTCTAA
GAAAGATTGGTATGATGTGAAAGCACCCGCTATGTTCAATATAAGAAATATTGGAAAGACGCTAGTCACCAGGACCCAAG
GAACCAAAATTGCATCTGATGGCCTCAAGGGTCGAGTGTTTGAAGTTAGTCTTGCTGATTTGCAGAATGATGAAGTTGCA
TTTAGAAAATTCAAGCTGATTACTGAAGATGTTCAGGGCAAAAACTGCCTGACTAACTTCCATGGCATGGATCTTACCCG
TGACAAAATGTGTTCCATGGTCAAAAAATGGCAGACAATGATTGAAGCTCATGTTGATGTCAAGACTACCGATGGTTACT
TGCTTCGTCTGTTCTGTGTTGGTTTTACTAAAAAACGCAACAATCAGATATGGAAGACCTCTTATGCTCAGCACCAACAG
GTCCGCCAAATCCGGAAGAAGATGATGGAAATCATGACCCGAGAGGTGCAGACAAATGACTTGAAAGAAGTGGTCAATAA
ATTGATTCCAGACAGCATTGGGAAAGACATAGAAAAGGCTTGCCAATCTATTTATCCTCTCCATGATGTCTTCGTTAGAA
AAGTAAAAATGCTGAAGAAGCCCAAGTTTGAATTGGGAAAACTCATGGAGCTTCATGGTGAAGGCAGTAGTTCTGGAAAA
GCCACTGGGGATGAGACAGGTGCTAAAGTTGAACGAGCTGATGGATATGAACCACCAGTCCAAGAATCTGTTTAA

ORF - retro_cjac_78 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 99.62 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMAVGKNKRLTKGGKKGAKKKVVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASDGLKGRVFEVS
MAVGKNKRLTKGGKKGAKKKVVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASDGLKGRVFEVS
RetrocopyMAVGKNKRLTKGGKKGAKKKVVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASDGLKGRVFEVS
ParentalLADLQNDEVAFRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTMIEAHVDVKTTDGYLLRLFCV
LADLQNDEVAFRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTMIEAHVDVKTTDGYLLRLFCV
RetrocopyLADLQNDEVAFRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTMIEAHVDVKTTDGYLLRLFCV
ParentalGFTKKRNNQIRKTSYAQHQQVRQIRKKMMEIMTREVQTNDLKEVVNKLIPDSIGKDIEKACQSIYPLHDV
GFTKKRNNQI.KTSYAQHQQVRQIRKKMMEIMTREVQTNDLKEVVNKLIPDSIGKDIEKACQSIYPLHDV
RetrocopyGFTKKRNNQIWKTSYAQHQQVRQIRKKMMEIMTREVQTNDLKEVVNKLIPDSIGKDIEKACQSIYPLHDV
ParentalFVRKVKMLKKPKFELGKLMELHGEGSSSGKATGDETGAKVERADGYEPPVQESV
FVRKVKMLKKPKFELGKLMELHGEGSSSGKATGDETGAKVERADGYEPPVQESV
RetrocopyFVRKVKMLKKPKFELGKLMELHGEGSSSGKATGDETGAKVERADGYEPPVQESV

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 .22 RPM 129 .26 RPM
SRP051959_heart 0 .19 RPM 106 .70 RPM
SRP051959_kidney 0 .29 RPM 127 .15 RPM
SRP051959_liver 0 .28 RPM 155 .03 RPM
SRP051959_lung 0 .15 RPM 131 .73 RPM
SRP051959_lymph_node 0 .53 RPM 217 .23 RPM
SRP051959_skeletal_muscle 0 .04 RPM 89 .97 RPM
SRP051959_spleen 0 .40 RPM 210 .59 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_78 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_78 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_78 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 19 parental genes, and 247 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG0000001842511 retrocopies
Bos taurus ENSBTAG000000099083 retrocopies
Canis familiaris ENSCAFG000000079907 retrocopies
Callithrix jacchus ENSCJAG00000002268 7 retrocopies
Dipodomys ordii ENSDORG0000000225010 retrocopies
Erinaceus europaeus ENSEEUG000000049944 retrocopies
Homo sapiens ENSG0000014542540 retrocopies
Microcebus murinus ENSMICG000000049219 retrocopies
Myotis lucifugus ENSMLUG000000147888 retrocopies
Macaca mulatta ENSMMUG000000218211 retrocopy
Monodelphis domestica ENSMODG000000009696 retrocopies
Mus musculus ENSMUSG000000280812 retrocopies
Nomascus leucogenys ENSNLEG0000000581526 retrocopies
Oryctolagus cuniculus ENSOCUG000000070111 retrocopy
Rattus norvegicus ENSRNOG000000118931 retrocopy
Sarcophilus harrisii ENSSHAG000000150882 retrocopies
Sus scrofa ENSSSCG000000090193 retrocopies
Tupaia belangeri ENSTBEG0000000296398 retrocopies
retro_tbel_1005, retro_tbel_11, retro_tbel_1119, retro_tbel_116, retro_tbel_1232, retro_tbel_1318, retro_tbel_133, retro_tbel_137, retro_tbel_1375, retro_tbel_1378, retro_tbel_1383, retro_tbel_1417, retro_tbel_1421, retro_tbel_1509, retro_tbel_1686, retro_tbel_1698, retro_tbel_172, retro_tbel_1720, retro_tbel_1721, retro_tbel_1744, retro_tbel_1814, retro_tbel_1829, retro_tbel_1856, retro_tbel_1896, retro_tbel_1948, retro_tbel_1960, retro_tbel_1999, retro_tbel_206, retro_tbel_2200, retro_tbel_2306, retro_tbel_2463, retro_tbel_2483, retro_tbel_2510, retro_tbel_2626, retro_tbel_2654, retro_tbel_2657, retro_tbel_2745, retro_tbel_2759, retro_tbel_2760, retro_tbel_2764, retro_tbel_281, retro_tbel_2857, retro_tbel_2957, retro_tbel_2959, retro_tbel_3114, retro_tbel_317, retro_tbel_3212, retro_tbel_3255, retro_tbel_3259, retro_tbel_3299, retro_tbel_336, retro_tbel_3372, retro_tbel_3416, retro_tbel_3471, retro_tbel_3486, retro_tbel_3513, retro_tbel_3558, retro_tbel_3613, retro_tbel_3631, retro_tbel_3655, retro_tbel_3705, retro_tbel_373, retro_tbel_375, retro_tbel_3755, retro_tbel_3786, retro_tbel_3815, retro_tbel_3823, retro_tbel_3832, retro_tbel_386, retro_tbel_3882, retro_tbel_39, retro_tbel_3947, retro_tbel_3966, retro_tbel_399, retro_tbel_4116, retro_tbel_4144, retro_tbel_4147, retro_tbel_4211, retro_tbel_4220, retro_tbel_423, retro_tbel_4294, retro_tbel_4304, retro_tbel_4347, retro_tbel_438, retro_tbel_4428, retro_tbel_445, retro_tbel_4579, retro_tbel_598, retro_tbel_619, retro_tbel_623, retro_tbel_671, retro_tbel_859, retro_tbel_90, retro_tbel_912, retro_tbel_92, retro_tbel_928, retro_tbel_956, retro_tbel_973,
Vicugna pacos ENSVPAG000000042358 retrocopies



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