RetrogeneDB ID:

retro_mmus_147

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:12:69372793..69373321(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMUSG00000044147
Aliases:Arf6, AI788669, AW496366
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:Arf3
Ensembl ID:ENSMUSG00000051853
Aliases:Arf3, 5430400P17Rik, AI854770
Description:ADP-ribosylation factor 3 [Source:MGI Symbol;Acc:MGI:99432]


Retrocopy-Parental alignment summary:






>retro_mmus_147
ATGGGGAAGGTGCTATCCAAGATCTTCGGGAACAAGGAAATGCGGATCCTCATGCTGGGCCTGGACGCAGCCGGCAAGAC
AACGATCCTGTACAAGTTGAAGCTGGGCCAATCGGTGACCACCATCCCCACGGTGGGCTTCAACGTGGAGACGGTGACTT
ACAAAAACGTCAAGTTCAACGTGTGGGATGTGGGCGGCCAGGACAAGATCCGGCCGCTCTGGCGGCATTACTACACCGGG
ACCCAGGGTCTGATCTTCGTGGTAGACTGCGCCGACCGCGACCGCATCGACGAGGCCCGCCAGGAGCTGCACCGCATTAT
CAATGACCGGGAGATGAGGGACGCCATCATCCTCATCTTCGCCAACAAGCAGGACCTGCCCGATGCCATGAAACCCCATG
AGATCCAGGAGAAACTGGGCCTGACCCGGATTCGGGACAGGAACTGGTATGTGCAGCCCTCCTGTGCCACCTCCGGGGAC
GGACTCTATGAGGGGCTCACATGGTTAACCTCTAACTACAAATCCTAA

ORF - retro_mmus_147 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 69.54 %
Parental protein coverage: 96.13 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalGNLLKSLIGKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIR
G..L....G.KEMRILM.GLDAAGKTTILYKLKLG..VTTIPT.GFNVETV.YKN..F.VWDVGGQDKIR
RetrocopyGKVLSKIFGNKEMRILMLGLDAAGKTTILYKLKLGQSVTTIPTVGFNVETVTYKNVKFNVWDVGGQDKIR
ParentalPLWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGL
PLWRHY...TQGLIFVVD..DR.R..EAR.EL.R.....E.RDA..L.FANKQDLP.AM...EI..KLGL
RetrocopyPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFANKQDLPDAMKPHEIQEKLGL
ParentalHSLRHRNWYIQATCATSGDGLYEGLDWLANQLKN
...R.RNWY.Q..CATSGDGLYEGL.WL....K.
RetrocopyTRIRDRNWYVQPSCATSGDGLYEGLTWLTSNYKS

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
SRP007412_brain 9 .70 RPM 1302 .01 RPM
SRP007412_cerebellum 9 .86 RPM 497 .61 RPM
SRP007412_heart 11 .02 RPM 58 .90 RPM
SRP007412_kidney 15 .15 RPM 244 .53 RPM
SRP007412_liver 15 .40 RPM 102 .00 RPM
SRP007412_testis 9 .88 RPM 157 .80 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_mmus_147 in 4 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF001XVA POLR2A 12:69371644..69373409
ENCFF001YIJ POLR2A 12:69370873..69373493
ENCFF001YJZ POLR2A 12:69370910..69372728
ENCFF001YKA POLR2A 12:69370883..69373491

EST - click to see more details

No EST(s) were mapped for retro_mmus_147 retrocopy.

TSS - click to see more details



TSS No. TSS Name TSS expression level (Expr) in TPM range:
no expression 0 < Expr ≤ 1 1 < Expr ≤ 5 5 < Expr ≤ 10 Expr > 10
TSS #1 TSS_2400286 libraries185 libraries589 libraries177 libraries35 libraries

The graphical summary, for retro_mmus_147 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Display detail expression values in each library
... or ...
Directly download all expression values

Lab - click to see more details

retro_mmus_147 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_147 has 12 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_36
Pan troglodytes retro_ptro_5
Gorilla gorilla retro_ggor_161
Pongo abelii retro_pabe_126
Macaca mulatta retro_mmul_174
Callithrix jacchus retro_cjac_300
Rattus norvegicus retro_rnor_272
Oryctolagus cuniculus retro_ocun_132
Bos taurus retro_btau_26
Sus scrofa retro_sscr_82
Canis familiaris retro_cfam_119
Equus caballus retro_ecab_106
Parental genes homology:
Parental genes homology involve 19 parental genes, and 27 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000082401 retrocopy
retro_acar_12,
Cavia porcellus ENSCPOG000000250741 retrocopy
retro_cpor_92,
Ciona savignyi ENSCSAVG000000070111 retrocopy
retro_csav_2,
Homo sapiens ENSG000001342871 retrocopy
retro_hsap_36,
Latimeria chalumnae ENSLACG000000190091 retrocopy
retro_lcha_10,
Loxodonta africana ENSLAFG000000042071 retrocopy
retro_lafr_115,
Macropus eugenii ENSMEUG000000050727 retrocopies
retro_meug_1036, retro_meug_1117, retro_meug_1857, retro_meug_29, retro_meug_395, retro_meug_616, retro_meug_946,
Microcebus murinus ENSMICG000000175451 retrocopy
retro_mmur_37,
Monodelphis domestica ENSMODG000000138041 retrocopy
retro_mdom_241,
Mus musculus ENSMUSG000000480761 retrocopy
retro_mmus_1718,
Mus musculus ENSMUSG00000051853 1 retrocopy
retro_mmus_147 ,
Mus musculus ENSMUSG000000624211 retrocopy
retro_mmus_2056,
Nomascus leucogenys ENSNLEG000000178592 retrocopies
retro_nleu_1348, retro_nleu_94,
Petromyzon marinus ENSPMAG000000005311 retrocopy
retro_pmar_5,
Rattus norvegicus ENSRNOG000000331551 retrocopy
retro_rnor_272,
Rattus norvegicus ENSRNOG000000480891 retrocopy
retro_rnor_2521,
Sarcophilus harrisii ENSSHAG000000036352 retrocopies
retro_shar_25, retro_shar_364,
Tetraodon nigroviridis ENSTNIG000000116851 retrocopy
retro_tnig_19,
Tursiops truncatus ENSTTRG000000046981 retrocopy
retro_ttru_1081,


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