RetrogeneDB ID:

retro_rnor_2161

Retrocopy
location
Organism:Rat (Rattus norvegicus)
Coordinates:5:100741056..100741760(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Snurf
Ensembl ID:ENSRNOG00000015976
Aliases:Snrpn, FE 294, FE 294 psi, FE294, FE294 psi
Description:Small nuclear ribonucleoprotein-associated protein N [Source:UniProtKB/Swiss-Prot;Acc:P63164]


Retrocopy-Parental alignment summary:






>retro_rnor_2161
ATGACTGTAGGTAAGAGTAGCAAGATGCTGCAGCATATTGACTATAGAACGAGATGTTTCCTGCAAGATGGAAGAATCTT
CATTGGCATCTTCAAGGCTTTTGACAAGCATATGAATTCGATCCTCTGTGATTGTGATGAATTCAGGAAGATCAAGCCAA
AGAATGAGAAACAGACAGAATGTGAAGAAAAAGTTTTGGGTCTGGTCTTGCTACGTGGAGAGAACTTGGTTTTCGTGACA
GTGGAGGGTCCATCTCCTAAAGATACTGGCATTACGCGTGTGCCACTTGCTGGTGCTGCAGGTGACCATGGGGTTGGAAG
AGCACCGGGCAGAGGAGTACCAGCAAGTGTACCTATTCCCCAAGCTCCTGCTGGATTACCAGGCCCTGTCCAAGGAGTTG
GAGGCCCATCTCAGCAGGTCATGAACCTACAGGGAAAAGGCACTGTTGCAGCTGCAGCTGTTGCTGCTACTGCTAGAATT
GCAAGAGCCCCAACCCAGTACCTGCCCGGACAGGGAACTCCACTTGTAGGCAGAGCAACCCCACCTCCAGGCATTATGGC
TCCTCCACCTGGTATGAGACCACCCATGGCCCCACCTATTGGCTTCCCTCTGCTTCAAGGACACCTATGCCCTCTCCAGG
AATGAGACCCCCTCCTCCAGGAATTAGAGGCTGACCTCCCCCAGGAATGTGTCCACCAATACCC

ORF - retro_rnor_2161 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.82 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMTVGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNAKQPEREEKRVLGLV
MTVGKSSKMLQHIDYR.RC.LQDGRIFIG.FKAFDKHMN.ILCDCDEFRKIKPKN.KQ.E.EEK.VLGLV
RetrocopyMTVGKSSKMLQHIDYRTRCFLQDGRIFIGIFKAFDKHMNSILCDCDEFRKIKPKNEKQTECEEK-VLGLV
ParentalLLRGENLVSMTVEGPPPKDTGIARVPLAGAAGGPGVGRAAGRGVPAGVPIPQAPAGLAGPVRGVGGPSQQ
LLRGENLV..TVEGP.PKDTGI.RVPLAGAAG..GVGRA.GRGVPA.VPIPQAPAGL.GPV.GVGGPSQQ
RetrocopyLLRGENLVFVTVEGPSPKDTGITRVPLAGAAGDHGVGRAPGRGVPASVPIPQAPAGLPGPVQGVGGPSQQ
ParentalVMTPQGRGTVAAAAVAATASIAGAPTQYPPGRGTPPPPVGRATPPPGIMAPPPGMRPPMGPPIG-LPPAR
VM..QG.GTVAAAAVAATA.IA.APTQY.PG.GT..P.VGRATPPPGIMAPPPGMRPPM.PPIG.LP.A.
RetrocopyVMNLQGKGTVAAAAVAATARIARAPTQYLPGQGT--PLVGRATPPPGIMAPPPGMRPPMAPPIG<LPSAS
ParentalGTPIGMPPPGMRPPPPGIRGPPPPGMRPPRP
.TP..MP.PGMRPPPPGIRG.PPPGM.PP.P
RetrocopyRTP--MPSPGMRPPPPGIRG*PPPGMCPPIP

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 448 .27 RPM
SRP017611_kidney 0 .00 RPM 13 .82 RPM
SRP017611_liver 0 .00 RPM 1 .28 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_2161 retrocopy.

TSS - click to see more details

Rattus norvegicus was not studied using FANTOM5 data.

Lab - click to see more details

retro_rnor_2161 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_rnor_2161 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 22 parental genes, and 53 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000070343 retrocopies
retro_amel_1048, retro_amel_714, retro_amel_839,
Bos taurus ENSBTAG000000082511 retrocopy
retro_btau_620,
Canis familiaris ENSCAFG000000101276 retrocopies
retro_cfam_1753, retro_cfam_1874, retro_cfam_2039, retro_cfam_627, retro_cfam_682, retro_cfam_752,
Choloepus hoffmanni ENSCHOG000000018462 retrocopies
retro_chof_2275, retro_chof_385,
Cavia porcellus ENSCPOG000000202701 retrocopy
retro_cpor_878,
Felis catus ENSFCAG000000222982 retrocopies
retro_fcat_1390, retro_fcat_1895,
Homo sapiens ENSG000001287391 retrocopy
retro_hsap_2580,
Gorilla gorilla ENSGGOG000000039881 retrocopy
retro_ggor_1615,
Loxodonta africana ENSLAFG000000094581 retrocopy
retro_lafr_1012,
Myotis lucifugus ENSMLUG000000233613 retrocopies
retro_mluc_1192, retro_mluc_1816, retro_mluc_2156,
Macaca mulatta ENSMMUG000000231391 retrocopy
retro_mmul_644,
Mustela putorius furoENSMPUG000000146381 retrocopy
retro_mputfur_1080,
Mus musculus ENSMUSG000000009483 retrocopies
retro_mmus_1285, retro_mmus_1733, retro_mmus_665,
Oryctolagus cuniculus ENSOCUG000000035324 retrocopies
retro_ocun_1291, retro_ocun_488, retro_ocun_689, retro_ocun_846,
Otolemur garnettii ENSOGAG000000073925 retrocopies
retro_ogar_1179, retro_ogar_3042, retro_ogar_3060, retro_ogar_475, retro_ogar_722,
Pongo abelii ENSPPYG000000062691 retrocopy
retro_pabe_1900,
Pan troglodytes ENSPTRG000000068261 retrocopy
retro_ptro_1507,
Rattus norvegicus ENSRNOG000000069612 retrocopies
retro_rnor_2825, retro_rnor_474,
Rattus norvegicus ENSRNOG00000015976 6 retrocopies
retro_rnor_1122, retro_rnor_1314, retro_rnor_1485, retro_rnor_2161 , retro_rnor_2462, retro_rnor_2517,
Sus scrofa ENSSSCG000000281242 retrocopies
retro_sscr_350, retro_sscr_405,
Ictidomys tridecemlineatus ENSSTOG000000013391 retrocopy
retro_itri_44,
Tursiops truncatus ENSTTRG000000109665 retrocopies
retro_ttru_1005, retro_ttru_1051, retro_ttru_1473, retro_ttru_580, retro_ttru_600,




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