RetrogeneDB ID:

retro_cjac_2653

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:5:108510953..108511252(-)
Located in intron of:ENSCJAG00000007258
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CMC1
Ensembl ID:ENSCJAG00000004272
Aliases:None
Description:COX assembly mitochondrial protein 1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:28783]


Retrocopy-Parental alignment summary:






>retro_cjac_2653
AAGCAACATCTCAGACATGTCGAAAAAGATGTTTTAATCCCTAAAATAATGACAGAAAAGGCCAGAGAGAGGTGTTCTGA
ACAAGTTCAAGATTTTACCAAATATTGCAATAATTCTGGAATCTTGATGGAGGAAAATGCTGGAAAGAAAATTCTACATT
GAAAAAACGTCTAACTGCTCAACTATAATGGTCCAGCCTTTTATGAAGAATGCAAAATGGAATACCTGAAGGAAGGAAGA
ATTCAGAAAAACTGGAATTTCTGCAAAGAGAAGGCCTCAGAAGCTTTCCCATAAGCCTG

ORF - retro_cjac_2653 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 63.11 %
Parental protein coverage: 94.34 %
Number of stop codons detected: 0
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalEQHLRHVEKDVLIPKKMREKARERCSEQIQDFTKCCQDSGVLMVI-KCRKENSALKECLTAY-YTDPAFY
.QHLRHVEKDVLIPK.M.EKARERCSEQ.QDFTK.C..SG.LM...KC.KENS.LK..LTA..Y..PAFY
RetrocopyKQHLRHVEKDVLIPKIMTEKARERCSEQVQDFTKYCNNSGILMEE<KCWKENSTLKKRLTAQ>YNGPAFY
ParentalEECKMEYLKE-REEFRRTGIPAKKRLQKLPTSM
EECKMEYLKE.R.............L...P.S.
RetrocopyEECKMEYLKE<RKNSEKLEFLQREGLRSFPISL

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 3 .77 RPM
SRP051959_heart 0 .00 RPM 5 .05 RPM
SRP051959_kidney 0 .00 RPM 4 .50 RPM
SRP051959_liver 0 .00 RPM 4 .87 RPM
SRP051959_lung 0 .00 RPM 6 .08 RPM
SRP051959_lymph_node 0 .00 RPM 11 .46 RPM
SRP051959_skeletal_muscle 0 .00 RPM 3 .56 RPM
SRP051959_spleen 0 .00 RPM 5 .36 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2653 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2653 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_2653 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 15 parental genes, and 39 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG00000004272 2 retrocopies
retro_cjac_2600, retro_cjac_2653 ,
Dasypus novemcinctus ENSDNOG000000189232 retrocopies
Homo sapiens ENSG000001871184 retrocopies
Gorilla gorilla ENSGGOG000000124064 retrocopies
Microcebus murinus ENSMICG000000117022 retrocopies
Myotis lucifugus ENSMLUG000000000442 retrocopies
Nomascus leucogenys ENSNLEG000000040664 retrocopies
Oryctolagus cuniculus ENSOCUG000000127932 retrocopies
Ochotona princeps ENSOPRG000000094741 retrocopy
Pongo abelii ENSPPYG000000140544 retrocopies
Pan troglodytes ENSPTRG000000147064 retrocopies
Rattus norvegicus ENSRNOG000000101491 retrocopy
Sorex araneus ENSSARG000000016291 retrocopy
Tupaia belangeri ENSTBEG000000025734 retrocopies
Tarsius syrichta ENSTSYG000000113712 retrocopies



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