RetrogeneDB ID:

retro_cjac_3155

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:8:96098210..96098444(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:BET1
Ensembl ID:ENSCJAG00000013720
Aliases:None
Description:Bet1 golgi vesicular membrane trafficking protein [Source:HGNC Symbol;Acc:14562]


Retrocopy-Parental alignment summary:






>retro_cjac_3155
ATGAGGCGTGCAGGCTTGGGTGAAGCAGGACCTCCTGGCAACTCTGGGAACGACGGCTAAGCTAACAGCAGGTATAGCAC
CTGTGAAGAAGAAAATGAGAGACTCGCTGAAAGTCTGAGAAGCAAAGTAGCTGCTATAAAATCTTTTCCCGTGGAAATAG
GCCATGGAGTTAAAACCCAAAATAAATTATCAGCTGAAACGGATTCACAACTGGATTCTACAATTGGATGTCTA

ORF - retro_cjac_3155 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 75.64 %
Parental protein coverage: 66.1 %
Number of stop codons detected: 1
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMRRAGLGEGVPPGNYGNYGYANSGYSACEEENERLTESLRSKVTAIKSLSIEIGHEVKTQNNLLAEMDSQ
MRRAGLGE..PPGN.GN.G.ANS.YS.CEEENERL.ESLRSKV.AIKS...EIGH.VKTQN.L.AE.DSQ
RetrocopyMRRAGLGEAGPPGNSGNDG*ANSRYSTCEEENERLAESLRSKVAAIKSFPVEIGHGVKTQNKLSAETDSQ
ParentalFDSTTGFL
.DST.G.L
RetrocopyLDSTIGCL

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 5 .84 RPM
SRP051959_heart 0 .02 RPM 6 .65 RPM
SRP051959_kidney 0 .00 RPM 16 .35 RPM
SRP051959_liver 0 .00 RPM 9 .92 RPM
SRP051959_lung 0 .03 RPM 8 .41 RPM
SRP051959_lymph_node 0 .09 RPM 6 .32 RPM
SRP051959_skeletal_muscle 0 .02 RPM 3 .78 RPM
SRP051959_spleen 0 .02 RPM 10 .04 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_3155 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_3155 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_3155 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 17 parental genes, and 29 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000034241 retrocopy
retro_btau_1054,
Choloepus hoffmanni ENSCHOG000000012761 retrocopy
retro_chof_2211,
Callithrix jacchus ENSCJAG000000008951 retrocopy
retro_cjac_3988,
Callithrix jacchus ENSCJAG00000013720 3 retrocopies
retro_cjac_1411, retro_cjac_2019, retro_cjac_3155 ,
Dasypus novemcinctus ENSDNOG000000010123 retrocopies
retro_dnov_1683, retro_dnov_393, retro_dnov_60,
Homo sapiens ENSG000001058291 retrocopy
retro_hsap_3809,
Gorilla gorilla ENSGGOG000000021761 retrocopy
retro_ggor_2560,
Loxodonta africana ENSLAFG000000005871 retrocopy
retro_lafr_1023,
Macaca mulatta ENSMMUG000000000071 retrocopy
retro_mmul_1656,
Nomascus leucogenys ENSNLEG000000154411 retrocopy
retro_nleu_2151,
Oryctolagus cuniculus ENSOCUG000000170292 retrocopies
retro_ocun_1116, retro_ocun_355,
Ochotona princeps ENSOPRG000000045364 retrocopies
retro_opri_201, retro_opri_249, retro_opri_388, retro_opri_880,
Pan troglodytes ENSPTRG000000194081 retrocopy
retro_ptro_2584,
Rattus norvegicus ENSRNOG000000110082 retrocopies
retro_rnor_2195, retro_rnor_2196,
Sus scrofa ENSSSCG000000153252 retrocopies
retro_sscr_455, retro_sscr_516,
Tupaia belangeri ENSTBEG000000007652 retrocopies
retro_tbel_3115, retro_tbel_4272,
Tarsius syrichta ENSTSYG000000097292 retrocopies
retro_tsyr_136, retro_tsyr_1843,


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