RetrogeneDB ID:

retro_cjac_456

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:1:115891641..115892117(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCJAG00000014622
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_456
ATGACTGGGTGAAAACTTGCTCTAAAAACCATTGACTGGGTAGCTTCTTGGGAGATCATACCGGGAAACCAAAAGGCCGT
TGTTAATTCCCTGAAATATTGGAATGAGACCCTCACCTCCAGGTTGGCTACTTTACCTGACAATCCACCAGCTATCGACT
GGGTTTACTACATGACCCATGTGGCCAAGGCAGGCCTAGGATATGATTTTGAGAAGTTGAATGTCCTGAAGCTTTCTGTA
CAAGAGAATAAATATACTGCCCAGGTGGATGCTGAGGAAAAAGAAGATGTGAAAACTTGTGCTGAGTGGGTGTCTGTCTC
AAAGGCCAGGATTGGAGAATATGAGAAACAGCTGGAGAAGATGAGTAACTTAATCCATTTGATAAGATGACCATTGAGGA
CTTAAATGAAGCTTTCCCAGAAACAAAATTAGCTAAGAAAAAGTAGCCCTAGTGGCCTCATCAACCAATCAAGAAT

ORF - retro_cjac_456 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.67 %
Parental protein coverage: 99.38 %
Number of stop codons detected: 3
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMAGRKLALKTIDWIAFWEIIPQNQKAIANSLKSWNEILTSRLAALPENPPSIDWAYYKANVAKAGLVDDF
M.G.KLALKTIDW.A.WEIIP.NQKA..NSLK.WNE.LTSRLA.LP.NPP.IDW.YY...VAKAGL..DF
RetrocopyMTG*KLALKTIDWVASWEIIPGNQKAVVNSLKYWNETLTSRLATLPDNPPAIDWVYYMTHVAKAGLGYDF
ParentalEKKFNALKVPIPEDPYTALVDAEEKEDVKSCAEWVSLSKARVVEYEKKMEKYKNLI-PFEQMTIEDLNEA
E.K.N.LK....E..YTA.VDAEEKEDVK.CAEWVS.SKAR..EYEK..EK..NLI.PF..MTIEDLNEA
RetrocopyE-KLNVLKLSVQENKYTAQVDAEEKEDVKTCAEWVSVSKARIGEYEKQLEKMSNLI<PFDKMTIEDLNEA
ParentalFPETKLDKQKYPYWPHQPIEN
FPETKL.K.K.P.WPHQPI.N
RetrocopyFPETKLAKKK*P*WPHQPIKN

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 .09 RPM 31 .37 RPM
SRP051959_heart 0 .02 RPM 68 .41 RPM
SRP051959_kidney 0 .00 RPM 48 .30 RPM
SRP051959_liver 0 .00 RPM 54 .97 RPM
SRP051959_lung 0 .07 RPM 18 .40 RPM
SRP051959_lymph_node 0 .00 RPM 18 .13 RPM
SRP051959_skeletal_muscle 0 .00 RPM 90 .15 RPM
SRP051959_spleen 0 .02 RPM 21 .87 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_456 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_456 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_456 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_4134
Pan troglodytes retro_ptro_2810
Gorilla gorilla retro_ggor_2778
Pongo abelii retro_pabe_3470

Parental genes homology:
Parental genes homology involve 29 parental genes, and 113 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000091156 retrocopies
Bos taurus ENSBTAG000000212275 retrocopies
Canis familiaris ENSCAFG000000047031 retrocopy
Callithrix jacchus ENSCJAG00000014622 15 retrocopies
Cavia porcellus ENSCPOG000000040223 retrocopies
Dasypus novemcinctus ENSDNOG000000069132 retrocopies
Equus caballus ENSECAG000000094872 retrocopies
Echinops telfairi ENSETEG000000032178 retrocopies
Felis catus ENSFCAG000000228882 retrocopies
Homo sapiens ENSG000001678634 retrocopies
Gorilla gorilla ENSGGOG000000137164 retrocopies
Macropus eugenii ENSMEUG000000093461 retrocopy
Microcebus murinus ENSMICG000000174844 retrocopies
Myotis lucifugus ENSMLUG000000106207 retrocopies
Macaca mulatta ENSMMUG000000116471 retrocopy
Mustela putorius furoENSMPUG000000140489 retrocopies
Mus musculus ENSMUSG000000345666 retrocopies
Nomascus leucogenys ENSNLEG000000005614 retrocopies
Oryctolagus cuniculus ENSOCUG000000155372 retrocopies
Otolemur garnettii ENSOGAG000000019904 retrocopies
Procavia capensis ENSPCAG000000153302 retrocopies
Pongo abelii ENSPPYG000000086154 retrocopies
Pan troglodytes ENSPTRG000000096284 retrocopies
Rattus norvegicus ENSRNOG000000036261 retrocopy
Sorex araneus ENSSARG000000133703 retrocopies
Sarcophilus harrisii ENSSHAG000000187082 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000151542 retrocopies
Tupaia belangeri ENSTBEG000000125453 retrocopies
Tursiops truncatus ENSTTRG000000026182 retrocopies



Copyright © RetrogeneDB 2014-2017