RetrogeneDB ID:

retro_cjac_1032

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:12:44299168..44299452(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL22
Ensembl ID:ENSCJAG00000000132
Aliases:None
Description:ribosomal protein L22 [Source:HGNC Symbol;Acc:10315]


Retrocopy-Parental alignment summary:






>retro_cjac_1032
ATGGCACCCATGAAAAAGCTTGTGGTGAAGGGGGGCCAAAAAAACACAGATTCTGAAGATCACTCTTGACTGCACCCACC
CCATAGAAGATGGAATCATGGGTGCTGCCTATTTTGAGCAGTGTTTGCAAGAGAGGGTCAAAGCAAATGGAAAAGCTGGG
AAACTTGGTCAGGGGCGTGGTGACCATTGAAAGGAGCAAGAGCAAGATCACAGTGACATCCGGGGTGACTTTTTCCAAAA
GGTATATGAAATATCACACTAAAAATGATTTGAAGAAGAAGAGT

ORF - retro_cjac_1032 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71.43 %
Parental protein coverage: 74.22 %
Number of stop codons detected: 0
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMAPVK-KLVAKGGKKKK-QVLKFTLDCTHPVEDGIMDAANFEQFLQERIKVNGKAGNLG-GGVVTIERSK
MAP.K.K....GG.KK..Q.LK.TLDCTHP.EDGIM.AA.FEQ.LQER.K.NGKAG.LG..GVVTIERSK
RetrocopyMAPMK<KACGEGGPKKH<QILKITLDCTHPIEDGIMGAAYFEQCLQERVKANGKAGKLG>RGVVTIERSK
ParentalSKITVTSEVPFSKRYLKYLTKKYLKKNN
SKITVTS.V.FSKRY.KY.TK..LKK..
RetrocopySKITVTSGVTFSKRYMKYHTKNDLKKKS

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 75 .77 RPM
SRP051959_heart 0 .00 RPM 79 .35 RPM
SRP051959_kidney 0 .00 RPM 85 .93 RPM
SRP051959_liver 0 .00 RPM 99 .12 RPM
SRP051959_lung 0 .00 RPM 102 .40 RPM
SRP051959_lymph_node 0 .00 RPM 147 .76 RPM
SRP051959_skeletal_muscle 0 .00 RPM 76 .52 RPM
SRP051959_spleen 0 .00 RPM 129 .01 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1032 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1032 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_1032 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 22 parental genes, and 184 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000098647 retrocopies
Bos taurus ENSBTAG000000144234 retrocopies
Choloepus hoffmanni ENSCHOG000000074772 retrocopies
Callithrix jacchus ENSCJAG00000000132 12 retrocopies
Callithrix jacchus ENSCJAG000000024271 retrocopy
Dasypus novemcinctus ENSDNOG000000131668 retrocopies
Felis catus ENSFCAG000000063203 retrocopies
Homo sapiens ENSG0000011625116 retrocopies
Gorilla gorilla ENSGGOG0000002773910 retrocopies
Loxodonta africana ENSLAFG000000063525 retrocopies
Macaca mulatta ENSMMUG0000001834712 retrocopies
Mustela putorius furoENSMPUG000000070876 retrocopies
Mus musculus ENSMUSG000000289365 retrocopies
Nomascus leucogenys ENSNLEG0000001033710 retrocopies
Otolemur garnettii ENSOGAG000000147767 retrocopies
Pongo abelii ENSPPYG0000000195111 retrocopies
Pan troglodytes ENSPTRG0000000007614 retrocopies
Rattus norvegicus ENSRNOG000000111045 retrocopies
Sus scrofa ENSSSCG000000033674 retrocopies
Tupaia belangeri ENSTBEG0000000917233 retrocopies
Tursiops truncatus ENSTTRG000000104888 retrocopies
Vicugna pacos ENSVPAG000000094661 retrocopy



Copyright © RetrogeneDB 2014-2017