RetrogeneDB ID:

retro_cjac_1826

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:2:96164527..96165020(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCJAG00000016272
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCJAG00000005912
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_1826
AATAAATTTCCATCAGAATATGTCCCGACTGTTTTTGACAACTATGCAGTCACAGTTATGATTGGTGAAGAACAATATAC
TCTTGGACTTTTTGATTCTGCAGGGCAAGAGGATTATGACAGATTACAACTGCTGAGTTATCCACAAACAGATATATTTC
TAGTCTGTTTTTCAGTAGTCTCTTTACCTTTGTTTGAAAATGTGAAAGAAAAGTGGGTGCCTAAGATAACTCACCGCTGT
CCAAAGACTTAATTCTTGCTTGTTGGGACTCCAATTAATCTCAGATGACGCCTCTACTATTGAGAAACTTGCCAAGAGCA
AACAGAAACCTATTATTCCAGAGACTGCTGAAAAGCTGGCCCATGACCTGAAGGCTGTCAAGTATGTGCAGCGTTTTGCA
CTTACACAGAAAGGCCAAAAGAATGTATCTGACAAAGCAATATTAGCTGCCCTGAAGGCTCCAGAACCGAAGAGGAGTCA
CAGGTGTGTGCTC

ORF - retro_cjac_1826 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 76.51 %
Parental protein coverage: 86.39 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalNKFPSEYVPTVFDNYAVTVMIGGEPYTLGLFDTAGQEDYDRLRPLSYPQTDVFLVCFSVVSPSSFENVKE
NKFPSEYVPTVFDNYAVTVMIG.E.YTLGLFD.AGQEDYDRL..LSYPQTD.FLVCFSVVS...FENVKE
RetrocopyNKFPSEYVPTVFDNYAVTVMIGEEQYTLGLFDSAGQEDYDRLQLLSYPQTDIFLVCFSVVSLPLFENVKE
ParentalKWVPEITHHCPKTPFLLV-GTQIDLRDDPSTIEKLAKNKQKPITPETAEKLARDLKAVKYVECSALTQRG
KWVP.ITH.CPKT.FLLV.G.Q....DD.STIEKLAK.KQKPI.PETAEKLA.DLKAVKYV...ALTQ.G
RetrocopyKWVPKITHRCPKT*FLLV>GLQL-ISDDASTIEKLAKSKQKPIIPETAEKLAHDLKAVKYVQRFALTQKG
ParentalLKNVFDEAILAALEPPETQPKRKCCI
.KNV.D.AILAAL..PE......C..
RetrocopyQKNVSDKAILAALKAPEPKRSHRCVL

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 66 .78 RPM
SRP051959_heart 0 .00 RPM 40 .97 RPM
SRP051959_kidney 0 .00 RPM 45 .24 RPM
SRP051959_liver 0 .00 RPM 34 .98 RPM
SRP051959_lung 0 .00 RPM 68 .11 RPM
SRP051959_lymph_node 0 .00 RPM 80 .73 RPM
SRP051959_skeletal_muscle 0 .00 RPM 27 .52 RPM
SRP051959_spleen 0 .00 RPM 80 .80 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1826 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1826 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_1826 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 31 parental genes, and 127 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000147075 retrocopies
Choloepus hoffmanni ENSCHOG0000000530610 retrocopies
Callithrix jacchus ENSCJAG000000006851 retrocopy
Callithrix jacchus ENSCJAG000000021444 retrocopies
Callithrix jacchus ENSCJAG00000005912 6 retrocopies
Callithrix jacchus ENSCJAG000000181941 retrocopy
Cavia porcellus ENSCPOG000000065434 retrocopies
Dipodomys ordii ENSDORG000000103743 retrocopies
Equus caballus ENSECAG000000191801 retrocopy
Echinops telfairi ENSETEG000000044431 retrocopy
Felis catus ENSFCAG000000048534 retrocopies
Homo sapiens ENSG000000708316 retrocopies
Gorilla gorilla ENSGGOG000000244395 retrocopies
Myotis lucifugus ENSMLUG000000133654 retrocopies
Macaca mulatta ENSMMUG000000220098 retrocopies
Monodelphis domestica ENSMODG000000160783 retrocopies
Mustela putorius furoENSMPUG000000159992 retrocopies
Mus musculus ENSMUSG000000066993 retrocopies
Nomascus leucogenys ENSNLEG000000081984 retrocopies
Oryctolagus cuniculus ENSOCUG000000099861 retrocopy
Otolemur garnettii ENSOGAG000000142611 retrocopy
Ochotona princeps ENSOPRG000000053312 retrocopies
Pongo abelii ENSPPYG000000017556 retrocopies
Rattus norvegicus ENSRNOG000000135361 retrocopy
Sorex araneus ENSSARG000000051843 retrocopies
Sus scrofa ENSSSCG000000035201 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000008054 retrocopies
Tupaia belangeri ENSTBEG0000000261417 retrocopies
Tarsius syrichta ENSTSYG0000000067911 retrocopies
Tursiops truncatus ENSTTRG000000057082 retrocopies
Vicugna pacos ENSVPAG000000069193 retrocopies



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