RetrogeneDB ID:

retro_cjac_872

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:11:106884633..106885334(+)
Located in intron of:ENSCJAG00000011325
Retrocopy
information
Ensembl ID:ENSCJAG00000011351
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCJAG00000007174
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_872
GTATATAATGTGGATGCTGGGCACAGAGCCGTCATCTTTGACCGATTCCGTGGAGTACAGGACATTGTGGTACAGGAAGG
GACTCACATTCTCATCCCGTGGGGAAAGAAACCAATTATCTTTGACTGCCGTTCTCCACCACGTATGTCCCAGTCATCAC
TGGCAGCAAAAATTCACAGATTGTCAACATCACCCTGCGCATCCTCTTCCGGCCCGTCACTAGCCAGCTTTCTCGCATCT
TCACCAGCATCAGAGGGAACCATGATGAGCATGTGCTGCCGTCCATCACTACCGAGATCCTCAAGTCCGTGGTGGCTCCC
TTTGATGCTGGAGAACTAATCACCTGGGGAGAGCTGGTCTCCAGGCGGGTGAACGGCGACCTTACGGATCAAGCAGCCAC
CTTTGGGCTCATCCTGGACGACGTGTCCTTGACACATCTGACCTTTGGAAAGGAGTTCACAGAAGCGGTGGAAGCCAAGC
AGGTGGCTCAGCAGGAAGCAGAGAAGGCCAGATTTGTGGTCAAAAAGGCTAAGCAGCAGAAAAAGGCAGCCATCATCTCT
GCTGAGGGCAATTCCAAGGCAGCCAAGCTGATCACCAATGCCCTGGCCTCCGCAGGGGACGGCCTGATCGAGCTGCACAA
GCTGGAAGCTACGGAGGATATCGCGTACCAGCTCTCAGACTCTCGGAATAGCACCTGCCTC

ORF - retro_cjac_872 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.4 %
Parental protein coverage: 86.03 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalLYNVDAGHRAVIFDRFRGVQDIVVGEGTHFLIPWVQKPIIFDCRSRPRN-VPVITGSKDLQNVNITLRIL
.YNVDAGHRAVIFDRFRGVQDIVV.EGTH.LIPW..KPIIFDCRS.PR..VPVITGSK..Q.VNITLRIL
RetrocopyVYNVDAGHRAVIFDRFRGVQDIVVQEGTHILIPWGKKPIIFDCRSPPRM<VPVITGSKNSQIVNITLRIL
ParentalFRPVASQLPRIFTSIGEDYDERVLPSITTEILKSVVARFDAGELITQRELVSRQVSDDLTERAATFGLIL
FRPV.SQL.RIFTSI....DE.VLPSITTEILKSVVA.FDAGELIT..ELVSR.V..DLT..AATFGLIL
RetrocopyFRPVTSQLSRIFTSIRGNHDEHVLPSITTEILKSVVAPFDAGELITWGELVSRRVNGDLTDQAATFGLIL
ParentalDDVSLTHLTFGKEFTEAVEAKQVAQQEAERARFVVEKAEQQKKAAIISAEGDSKAAELIANSLATAGDGL
DDVSLTHLTFGKEFTEAVEAKQVAQQEAE.ARFVV.KA.QQKKAAIISAEG.SKAA.LI.N.LA.AGDGL
RetrocopyDDVSLTHLTFGKEFTEAVEAKQVAQQEAEKARFVVKKAKQQKKAAIISAEGNSKAAKLITNALASAGDGL
ParentalIELRKLEAAEDIAYQLSRSRNITYL
IEL.KLEA.EDIAYQLS.SRN.T.L
RetrocopyIELHKLEATEDIAYQLSDSRNSTCL

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 1 .49 RPM 25 .23 RPM
SRP051959_heart 0 .84 RPM 28 .57 RPM
SRP051959_kidney 1 .49 RPM 39 .49 RPM
SRP051959_liver 0 .74 RPM 38 .12 RPM
SRP051959_lung 1 .63 RPM 15 .55 RPM
SRP051959_lymph_node 1 .26 RPM 13 .06 RPM
SRP051959_skeletal_muscle 0 .90 RPM 33 .89 RPM
SRP051959_spleen 1 .26 RPM 14 .35 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_872 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_872 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_872 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 26 parental genes, and 165 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000047971 retrocopy
Ailuropoda melanoleuca ENSAMEG000000123641 retrocopy
Bos taurus ENSBTAG000000171201 retrocopy
Canis familiaris ENSCAFG000000169261 retrocopy
Choloepus hoffmanni ENSCHOG000000075882 retrocopies
Callithrix jacchus ENSCJAG00000007174 22 retrocopies
Erinaceus europaeus ENSEEUG000000064813 retrocopies
Homo sapiens ENSG0000016708515 retrocopies
Gorilla gorilla ENSGGOG0000002800212 retrocopies
Macropus eugenii ENSMEUG000000051221 retrocopy
Microcebus murinus ENSMICG000000069669 retrocopies
Myotis lucifugus ENSMLUG000000082032 retrocopies
Macaca mulatta ENSMMUG0000000015613 retrocopies
Monodelphis domestica ENSMODG000000122101 retrocopy
Mus musculus ENSMUSG000000388458 retrocopies
Nomascus leucogenys ENSNLEG0000000297813 retrocopies
Oryctolagus cuniculus ENSOCUG000000072091 retrocopy
Otolemur garnettii ENSOGAG000000270151 retrocopy
Ochotona princeps ENSOPRG000000008682 retrocopies
Procavia capensis ENSPCAG000000088511 retrocopy
Pongo abelii ENSPPYG0000000892016 retrocopies
Pan troglodytes ENSPTRG0000000937614 retrocopies
Rattus norvegicus ENSRNOG0000004679918 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000199292 retrocopies
Tupaia belangeri ENSTBEG000000105374 retrocopies
Tursiops truncatus ENSTTRG000000108361 retrocopy



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