RetrogeneDB ID:

retro_cjac_316

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:13:57607971..57608490(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCJAG00000023166
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCJAG00000016338
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_316
ATGGCTTCCAGCTTTAAGAAGTCCAGCGCCGCTGCCACCAGCCAGAAGAGAAAGGTGGTGCCTAAGCCCGAGCTCACTGA
AGATCAGAAGCAAGAAATTAGAGAAGCGTTTGACCTCTTTGACGTCGACGGAAGCGGGACCATCGATGTGAAGGAGCTGA
AGGTGGCCATGAGAGCGCTGGGCTTCGAACCCAGGAAGGAAGAGATGAAGAAGATGATCTCCGAGGTGGACAAGGAGGGC
ACGGGGAAGATCAGCTTCAATGACTTCCTGGCCGTGATGACTCAGAAGATGTCCGAGAAGGACACCAAAGAAGAAATCCT
GAAGGCCTTCAGGCTCTTTGATGACGATGAGACTGGGAAGATCTCGTTCAAAAACCTGAAGCGTGTGGCCAACGAGCTGG
GGGAAAACCTCACGGACGAGGAGCTGCAGGAGATGATCGACGAAGCTGATCGGGACGGGGACGGCGAAGTGAACGAGGAG
GAGTTCCTTCGGATCATGAGGAAGACCAACCTTTACTGA

ORF - retro_cjac_316 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.72 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMASSFKKANMASSAQRKRMSPKPELTEEQKQEIREAFDLFDADGTGSIDVKELKVAMRALGFEPKKEEIK
MASSFKK...A...Q.....PKPELTE.QKQEIREAFDLFD.DG.G.IDVKELKVAMRALGFEP.KEE.K
RetrocopyMASSFKKSSAAATSQKRKVVPKPELTEDQKQEIREAFDLFDVDGSGTIDVKELKVAMRALGFEPRKEEMK
ParentalKMISEIDKEGTGKMNFGDFLTVMTQKMSEKDTKEEILKAFKLFDDDETGKISFKNLKRVAKELGENLTDE
KMISE.DKEGTGK..F.DFL.VMTQKMSEKDTKEEILKAF.LFDDDETGKISFKNLKRVA.ELGENLTDE
RetrocopyKMISEVDKEGTGKISFNDFLAVMTQKMSEKDTKEEILKAFRLFDDDETGKISFKNLKRVANELGENLTDE
ParentalELQEMIDEADRDGDGEVSEQEFLRIMKKTSLY
ELQEMIDEADRDGDGEV.E.EFLRIM.KT.LY
RetrocopyELQEMIDEADRDGDGEVNEEEFLRIMRKTNLY

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(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 4 .95 RPM
SRP051959_heart 0 .00 RPM 6 .31 RPM
SRP051959_kidney 0 .00 RPM 14 .44 RPM
SRP051959_liver 0 .00 RPM 7 .04 RPM
SRP051959_lung 0 .00 RPM 13 .23 RPM
SRP051959_lymph_node 0 .00 RPM 6 .28 RPM
SRP051959_skeletal_muscle 0 .00 RPM 6 .07 RPM
SRP051959_spleen 0 .00 RPM 7 .56 RPM

ChIP-Seq - click to see more details

Callithrix jacchus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_cjac_316 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_316 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_316 has 9 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_71
Pan troglodytes retro_ptro_108
Gorilla gorilla retro_ggor_74
Pongo abelii retro_pabe_58
Macaca mulatta retro_mmul_176
Oryctolagus cuniculus retro_ocun_180
Bos taurus retro_btau_170
Canis familiaris retro_cfam_199
Equus caballus retro_ecab_49
Parental genes homology:
Parental genes homology involve 29 parental genes, and 45 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000003641 retrocopy
retro_amel_56,
Bos taurus ENSBTAG000000078441 retrocopy
retro_btau_170,
Canis familiaris ENSCAFG000000191701 retrocopy
retro_cfam_199,
Choloepus hoffmanni ENSCHOG000000102441 retrocopy
retro_chof_39,
Callithrix jacchus ENSCJAG00000016338 3 retrocopies
retro_cjac_106, retro_cjac_185, retro_cjac_316 ,
Callithrix jacchus ENSCJAG000000169071 retrocopy
retro_cjac_3944,
Cavia porcellus ENSCPOG000000120812 retrocopies
retro_cpor_1250, retro_cpor_21,
Equus caballus ENSECAG000000007961 retrocopy
retro_ecab_49,
Felis catus ENSFCAG000000049011 retrocopy
retro_fcat_47,
Homo sapiens ENSG000001474001 retrocopy
retro_hsap_71,
Gorilla gorilla ENSGGOG000000113781 retrocopy
retro_ggor_74,
Loxodonta africana ENSLAFG000000144241 retrocopy
retro_lafr_121,
Microcebus murinus ENSMICG000000058622 retrocopies
retro_mmur_122, retro_mmur_21,
Myotis lucifugus ENSMLUG000000145202 retrocopies
retro_mluc_320, retro_mluc_370,
Macaca mulatta ENSMMUG000000207432 retrocopies
retro_mmul_1127, retro_mmul_176,
Mustela putorius furoENSMPUG000000118581 retrocopy
retro_mputfur_386,
Mus musculus ENSMUSG000000313472 retrocopies
retro_mmus_107, retro_mmus_838,
Nomascus leucogenys ENSNLEG000000138601 retrocopy
retro_nleu_1221,
Oryctolagus cuniculus ENSOCUG000000078971 retrocopy
retro_ocun_180,
Otolemur garnettii ENSOGAG000000053011 retrocopy
retro_ogar_236,
Procavia capensis ENSPCAG000000032031 retrocopy
retro_pcap_149,
Procavia capensis ENSPCAG000000077781 retrocopy
retro_pcap_364,
Pongo abelii ENSPPYG000000208331 retrocopy
retro_pabe_58,
Pan troglodytes ENSPTRG000000223891 retrocopy
retro_ptro_108,
Rattus norvegicus ENSRNOG000000170595 retrocopies
retro_rnor_2376, retro_rnor_2394, retro_rnor_2920, retro_rnor_304, retro_rnor_775,
Sus scrofa ENSSSCG000000127573 retrocopies
retro_sscr_1175, retro_sscr_57, retro_sscr_822,
Ictidomys tridecemlineatus ENSSTOG000000238532 retrocopies
retro_itri_636, retro_itri_91,
Tarsius syrichta ENSTSYG000000038312 retrocopies
retro_tsyr_1142, retro_tsyr_36,
Tursiops truncatus ENSTTRG000000012362 retrocopies
retro_ttru_32, retro_ttru_335,


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