RetrogeneDB ID:

retro_cjac_1226

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:14:79825215..79825575(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:ACP1
Ensembl ID:ENSCJAG00000011663
Aliases:None
Description:acid phosphatase 1, soluble [Source:HGNC Symbol;Acc:122]


Retrocopy-Parental alignment summary:






>retro_cjac_1226
GGCCCCTGGGCACGTGGGAAGGTGGCAGAGCTGGCTACCAAGTCCGTGCTGTTTGTGTGTCTGGGTAACATTTGTCGATC
ACCCATTGCAGAAGCAGTTTTCAGGAAACTTGTAACTGATCAAAAAATCTCAGACAATTGGAGGGTAGACAGTGCGGCGA
CTTCCGGGTATGAGGGCGGGAAACCCCTGACTACTGAGGGCAGAGCGGCATGAAGAGGCATGGCATTCCCCATGAACCAC
GTGTCCCGGAAGATTACCAAAGAAGATTTTGCCACATTTGATTATATACTATGTATGGATGAGAGCAATCTGAGAGATTT
GAATAGAAAAAGTAATCGAGTTAAAACCTGCAGAGCTAGG

ORF - retro_cjac_1226 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82.79 %
Parental protein coverage: 72.73 %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalGATTRGKMAEPAAKSVLFVCLGNICRSPIAEAVFRKLVTDQNISENWRVDSAATSGYEIGNP-PDYRGQN
G...RGK.AE.A.KSVLFVCLGNICRSPIAEAVFRKLVTDQ.IS.NWRVDSAATSGYE.G.P.PDY.GQ.
RetrocopyGPWARGKVAELATKSVLFVCLGNICRSPIAEAVFRKLVTDQKISDNWRVDSAATSGYEGGKP<PDY*GQS
ParentalCMKRHGI-PMSHVARQITKEDFATFDYILCMDESNLRDLNRKSNQVKTCKAK
.MKRHGI.PM.HV.R.ITKEDFATFDYILCMDESNLRDLNRKSN.VKTC.A.
RetrocopyGMKRHGI>PMNHVSRKITKEDFATFDYILCMDESNLRDLNRKSNRVKTCRAR

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 .02 RPM 9 .94 RPM
SRP051959_heart 0 .39 RPM 7 .44 RPM
SRP051959_kidney 0 .02 RPM 12 .47 RPM
SRP051959_liver 0 .00 RPM 11 .31 RPM
SRP051959_lung 0 .03 RPM 9 .58 RPM
SRP051959_lymph_node 0 .02 RPM 9 .09 RPM
SRP051959_skeletal_muscle 0 .37 RPM 8 .45 RPM
SRP051959_spleen 0 .11 RPM 8 .63 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1226 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1226 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_1226 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 25 parental genes, and 250 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000095542 retrocopies
Bos taurus ENSBTAG000000204984 retrocopies
Choloepus hoffmanni ENSCHOG0000000389194 retrocopies
retro_chof_1010, retro_chof_1053, retro_chof_1073, retro_chof_1099, retro_chof_1100, retro_chof_1144, retro_chof_119, retro_chof_1190, retro_chof_121, retro_chof_1259, retro_chof_1265, retro_chof_1275, retro_chof_1330, retro_chof_1351, retro_chof_1359, retro_chof_1389, retro_chof_1390, retro_chof_1412, retro_chof_142, retro_chof_1444, retro_chof_1447, retro_chof_1508, retro_chof_1567, retro_chof_1570, retro_chof_1593, retro_chof_1632, retro_chof_1633, retro_chof_1658, retro_chof_1684, retro_chof_169, retro_chof_1698, retro_chof_17, retro_chof_1716, retro_chof_174, retro_chof_1799, retro_chof_1802, retro_chof_1815, retro_chof_1833, retro_chof_1838, retro_chof_1864, retro_chof_1941, retro_chof_1956, retro_chof_1993, retro_chof_2012, retro_chof_2041, retro_chof_2044, retro_chof_2091, retro_chof_2165, retro_chof_2192, retro_chof_2208, retro_chof_2228, retro_chof_2259, retro_chof_2344, retro_chof_2378, retro_chof_2384, retro_chof_2443, retro_chof_245, retro_chof_2478, retro_chof_2512, retro_chof_2532, retro_chof_2542, retro_chof_2551, retro_chof_261, retro_chof_262, retro_chof_2622, retro_chof_2636, retro_chof_2643, retro_chof_2653, retro_chof_2654, retro_chof_2678, retro_chof_2701, retro_chof_2705, retro_chof_2707, retro_chof_319, retro_chof_377, retro_chof_460, retro_chof_598, retro_chof_603, retro_chof_649, retro_chof_650, retro_chof_66, retro_chof_727, retro_chof_80, retro_chof_803, retro_chof_83, retro_chof_842, retro_chof_934, retro_chof_939, retro_chof_958, retro_chof_962, retro_chof_986, retro_chof_991, retro_chof_994, retro_chof_999,
Callithrix jacchus ENSCJAG00000011663 5 retrocopies
Dasypus novemcinctus ENSDNOG0000001738232 retrocopies
Equus caballus ENSECAG000000100791 retrocopy
Echinops telfairi ENSETEG0000001376418 retrocopies
Felis catus ENSFCAG000000267171 retrocopy
Homo sapiens ENSG000001437275 retrocopies
Gorilla gorilla ENSGGOG000000155775 retrocopies
Loxodonta africana ENSLAFG000000029664 retrocopies
Macropus eugenii ENSMEUG000000107333 retrocopies
Myotis lucifugus ENSMLUG000000177074 retrocopies
Macaca mulatta ENSMMUG000000170972 retrocopies
Monodelphis domestica ENSMODG000000257643 retrocopies
Mustela putorius furoENSMPUG000000127872 retrocopies
Mus musculus ENSMUSG0000004457311 retrocopies
Nomascus leucogenys ENSNLEG000000083596 retrocopies
Oryctolagus cuniculus ENSOCUG0000001287611 retrocopies
Otolemur garnettii ENSOGAG000000003015 retrocopies
Pongo abelii ENSPPYG000000126946 retrocopies
Pan troglodytes ENSPTRG000000116055 retrocopies
Rattus norvegicus ENSRNOG0000000526011 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000025203 retrocopies
Tarsius syrichta ENSTSYG000000048647 retrocopies



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