RetrogeneDB ID:

retro_cjac_1222

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:14:73138400..73138738(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPLP1
Ensembl ID:ENSCJAG00000032919
Aliases:None
Description:ribosomal protein, large, P1 [Source:HGNC Symbol;Acc:10372]


Retrocopy-Parental alignment summary:






>retro_cjac_1222
ATGGCCTTAGTCTCCAAGCTCACCTGCATCTACTTGGCCCTCATTCTGCACGACGATGAGGTAACCGTTACAGAAGTTAA
GATCAATGCCCTCATTAAAGCAGCAGGTGTAAATGTTGAACGTTTTGGCCTGGCTTGTTTGCAAAGGCCCTGGCCAGCAT
CAACATTGGGAGCCTCATCTGCAATGTAGAGGCTGGTGGGCTTGCTCCAGCAGCAGGTGTTGCTCCAGCAGGAGGTCCTG
CCCCCTCCACCACTGCTGCTCCAGCTGAGGAGAAAGTGGAAGCAAAGAAAGAAGAATCCGAGGAGTCTGATGATGACATG
GGCTTTGGTCTTTTTGAC

ORF - retro_cjac_1222 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.83 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMASVSELACIYSALILHDDEVTVTEDKINALIKAAGVNVE-PFWPGLFAKALANVNIGSLICNVGAGGPA
MA.VS.L.CIY.ALILHDDEVTVTE.KINALIKAAGVNVE..FWPGLFAKALA..NIGSLICNV.AGG.A
RetrocopyMALVSKLTCIYLALILHDDEVTVTEVKINALIKAAGVNVE<TFWPGLFAKALASINIGSLICNVEAGGLA
ParentalPAAGAAPAGGPAPSTAAAPAEEKKVEAKKEESEESDDDMGFGLFD
PAAG.APAGGPAPST.AAPAEE.KVEAKKEESEESDDDMGFGLFD
RetrocopyPAAGVAPAGGPAPSTTAAPAEE-KVEAKKEESEESDDDMGFGLFD

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 .00 RPM 107 .48 RPM
SRP051959_heart 0 .00 RPM 102 .58 RPM
SRP051959_kidney 0 .00 RPM 120 .09 RPM
SRP051959_liver 0 .00 RPM 96 .48 RPM
SRP051959_lung 0 .02 RPM 121 .91 RPM
SRP051959_lymph_node 0 .00 RPM 168 .97 RPM
SRP051959_skeletal_muscle 0 .00 RPM 176 .65 RPM
SRP051959_spleen 0 .00 RPM 171 .41 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1222 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1222 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_1222 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 22 parental genes, and 199 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000183204 retrocopies
Callithrix jacchus ENSCJAG00000032919 19 retrocopies
Equus caballus ENSECAG000000085424 retrocopies
Homo sapiens ENSG0000013781818 retrocopies
Gorilla gorilla ENSGGOG0000000398013 retrocopies
Latimeria chalumnae ENSLACG000000126301 retrocopy
Macropus eugenii ENSMEUG000000152776 retrocopies
Myotis lucifugus ENSMLUG0000001054233 retrocopies
Macaca mulatta ENSMMUG000000148887 retrocopies
Monodelphis domestica ENSMODG000000092091 retrocopy
Mustela putorius furoENSMPUG0000000020413 retrocopies
Mus musculus ENSMUSG000000078926 retrocopies
Oryctolagus cuniculus ENSOCUG000000150878 retrocopies
Otolemur garnettii ENSOGAG0000002964119 retrocopies
Ochotona princeps ENSOPRG0000000116311 retrocopies
Procavia capensis ENSPCAG000000145957 retrocopies
Pongo abelii ENSPPYG000000066015 retrocopies
Pan troglodytes ENSPTRG000000072281 retrocopy
Rattus norvegicus ENSRNOG000000119556 retrocopies
Rattus norvegicus ENSRNOG000000138743 retrocopies
Sarcophilus harrisii ENSSHAG000000148186 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000278938 retrocopies



Copyright © RetrogeneDB 2014-2017