RetrogeneDB ID:

retro_rnor_2521

Retrocopy
location
Organism:Rat (Rattus norvegicus)
Coordinates:7:57049916..57050458(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:ARF1
Ensembl ID:ENSRNOG00000048089
Aliases:None
Description:ADP-ribosylation factor 1 [Source:UniProtKB/Swiss-Prot;Acc:P84079]


Retrocopy-Parental alignment summary:






>retro_rnor_2521
ATGGGCTTTATCTTTGCAAACATTTTCAACGGCCCTTTTGGCAAAAAAGAAATAAGCATTTTCATGGTGAGCCCGGATGC
TACAGGGAAGACCAAAATTCTATACAATCTGAAGCTGGGCAAAATTGTGACCACCATTCCCACCATGGTTTCAACGTAGA
GACTGTTGGATACAAGAATATCAGCTTCACGGTGTGAGATGTGGGCGACCAGGACAAGATCCCACCACTGTGGCGCCGCT
ATTTCCAGAACACACAAGGTTTGATCTTCATAGTGGACGGCAATGACAGAGAGCGTGTGAACGGGGCCGGTGATGAAGAG
CTCCTGAGTATGCTCGCTGAGGATGAGCTCCGAGATACTGTTTTCTTGGTGTTTGCCAACAAGCAGGACCTCCCCAAGCC
ATAAATGAGGCCAAAATCACAGACAAGCTGGTACTGCACTCAACGTCACAAGAACTGGTATATTCAGGCTCTCTGTGCCG
CCAGTGGGGACGGGCTCAATGAAGGACTAGACTGGCTGTCTAATCAGCTCTGGAACCAGAAG

ORF - retro_rnor_2521 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 70.33 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 2
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalMGNIFGNLLKSLIGKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTI-GFNVETVEYKNISFTVWDVG
MG.IF.N......GKKE..I.MV..DA.GKT.ILY.LKLG.IVTTIPT..GFNVETV.YKNISFTV.DVG
RetrocopyMGFIFANIFNGPFGKKEISIFMVSPDATGKTKILYNLKLGKIVTTIPTM<GFNVETVGYKNISFTV*DVG
ParentalGQDKIRPLWRHYFQNTQGLIFVVDSNDRERVNEAR-EELMRMLAEDELRDAVLLVFANKQDLPNA-MNAA
.QDKI.PLWR.YFQNTQGLIF.VD.NDRERVN.A..EEL..MLAEDELRD.V.LVFANKQDLP...M...
RetrocopyDQDKIPPLWRRYFQNTQGLIFIVDGNDRERVNGAGDEELLSMLAEDELRDTVFLVFANKQDLPKP*MRPK
ParentalEITDSLHSLRHRNWYIQATCATSGDGLYEGLDWLANQLKNKK
..T......RH.NWYIQA.CA.SGDGL.EGLDWL.NQL.N.K
RetrocopySQTSWYCTQRHKNWYIQALCAASGDGLNEGLDWLSNQLWNQK

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
SRP017611_brain 0 .00 RPM 30 .12 RPM
SRP017611_kidney 0 .00 RPM 4 .54 RPM
SRP017611_liver 0 .00 RPM 1 .48 RPM

ChIP-Seq - click to see more details

Rattus norvegicus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_rnor_2521 retrocopy.

TSS - click to see more details

Rattus norvegicus was not studied using FANTOM5 data.

Lab - click to see more details

retro_rnor_2521 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_rnor_2521 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 29 parental genes, and 43 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000082401 retrocopy
retro_acar_12,
Ailuropoda melanoleuca ENSAMEG000000070422 retrocopies
retro_amel_28, retro_amel_70,
Canis familiaris ENSCAFG000000087671 retrocopy
retro_cfam_119,
Cavia porcellus ENSCPOG000000250741 retrocopy
retro_cpor_92,
Ciona savignyi ENSCSAVG000000070111 retrocopy
retro_csav_2,
Felis catus ENSFCAG000000000882 retrocopies
retro_fcat_2, retro_fcat_59,
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,
Myotis lucifugus ENSMLUG000000298461 retrocopy
retro_mluc_119,
Macaca mulatta ENSMMUG000000069681 retrocopy
retro_mmul_174,
Monodelphis domestica ENSMODG000000138041 retrocopy
retro_mdom_241,
Mustela putorius furoENSMPUG000000147301 retrocopy
retro_mputfur_86,
Mus musculus ENSMUSG000000518531 retrocopy
retro_mmus_147,
Nomascus leucogenys ENSNLEG000000178592 retrocopies
retro_nleu_1348, retro_nleu_94,
Ochotona princeps ENSOPRG000000074112 retrocopies
retro_opri_13, retro_opri_3,
Petromyzon marinus ENSPMAG000000005311 retrocopy
retro_pmar_5,
Pongo abelii ENSPPYG000000044731 retrocopy
retro_pabe_126,
Pteropus vampyrus ENSPVAG000000046261 retrocopy
retro_pvam_7,
Rattus norvegicus ENSRNOG000000126232 retrocopies
retro_rnor_1036, retro_rnor_1884,
Rattus norvegicus ENSRNOG000000305913 retrocopies
retro_rnor_1268, retro_rnor_1348, retro_rnor_1950,
Rattus norvegicus ENSRNOG000000331551 retrocopy
retro_rnor_272,
Rattus norvegicus ENSRNOG00000048089 1 retrocopy
retro_rnor_2521 ,
Sarcophilus harrisii ENSSHAG000000036352 retrocopies
retro_shar_25, retro_shar_364,
Ictidomys tridecemlineatus ENSSTOG000000042951 retrocopy
retro_itri_175,
Tetraodon nigroviridis ENSTNIG000000116851 retrocopy
retro_tnig_19,
Tursiops truncatus ENSTTRG000000046981 retrocopy
retro_ttru_1081,


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