RetrogeneDB ID:

retro_rnor_1133

Retrocopy
location
Organism:Rat (Rattus norvegicus)
Coordinates:15:111267452..111268144(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Eif3e
Ensembl ID:ENSRNOG00000027690
Aliases:Eif3e, Eif3s6
Description:Eukaryotic translation initiation factor 3 subunit E [Source:UniProtKB/Swiss-Prot;Acc:Q641X8]


Retrocopy-Parental alignment summary:






>retro_rnor_1133
CTGGTCTCTGTTTGTTTGTTTTTTTTTTTCAGCCATCCAAAAGGACATGATAATATTATTGATCTCTTCCTTTACCAACT
ACAGTACCTTAATGCAATTCAGAAAATGTGTCCACATAGTCTCCGCTATTTGACCACTGCCATAATAACCAACAAAGATA
TGCAGAAACGCTGGCAGGTGCTGAAAGATCTAGTGAAAGTTATTCAACAGGAGTCTTACACATATAAAGAACCAATTACA
GAATTTGTTGAATGCCTATATGTTAACTTTGATTTTGATGGAGCTCAGAAAAAGGTAAGAGAATGTGAATTAGTGCCTGT
GAATGACTTCTTCCTGGTAGCATGTCTTGAGGACTTCATTGAGAATGTCCGTCTCTTCATATTTGAGAGTTTCTATCGTA
TCCACCAGTGTATCAGCATTAATATGTTAGCAGAGAAACTTAATATGACTCCAAGAGAAGCTGAAAGATGGATTGTGAAT
TTGATTAGAAATGTGAGGCTGGATGCCAGGACTGATTCTAAACTAGGTTATGTGGTAATGGGCAACAATGCAGTCTCACC
CTACCAGCAAGGGATTGAAAAGACTAAAAGTCTTTGTTGTAGAAGCCAAATATTGGCCATGAATATAGAAAAGAAACTTA
ACAGAACAGTAGACCAGAGGCTCCCAACTGGGCAACCCAAGATTCCGGCTTC

ORF - retro_rnor_1133 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.48 %
Parental protein coverage: 51.91 %
Number of stop codons detected: 0
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalLIHWSLFVFFNHPKGRDNIIDLFLYQPQYLNAIQTMCPHILRYLTTAVITNKDVRKRRQVLKDLVKVIQQ
L....L.....HPKG.DNIIDLFLYQ.QYLNAIQ.MCPH.LRYLTTA.ITNKD..KR.QVLKDLVKVIQQ
RetrocopyLVSVCLXXXXSHPKGHDNIIDLFLYQLQYLNAIQKMCPHSLRYLTTAIITNKDMQKRWQVLKDLVKVIQQ
ParentalESYTYKDPITEFVECLYVNFDFDGAQKKLRECESVLVNDFFLVACLEDFIENARLFIFETFCRIHQCISI
ESYTYK.PITEFVECLYVNFDFDGAQKK.RECE.V.VNDFFLVACLEDFIEN.RLFIFE.F.RIHQCISI
RetrocopyESYTYKEPITEFVECLYVNFDFDGAQKKVRECELVPVNDFFLVACLEDFIENVRLFIFESFYRIHQCISI
ParentalNMLADKLNMTPEEAERWIVNLIRNARLDAKIDSKLGHVVMGNNAVSPYQQVIEKTKSLSFRSQMLAMNIE
NMLA.KLNMTP.EAERWIVNLIRN.RLDA..DSKLG.VVMGNNAVSPYQQ.IEKTKSL..RSQ.LAMNIE
RetrocopyNMLAEKLNMTPREAERWIVNLIRNVRLDARTDSKLGYVVMGNNAVSPYQQGIEKTKSLCCRSQILAMNIE
ParentalKKLN-QNSRSEAPNWATQDSGF
KKLN.QNSR.EAPNWATQDSGF
RetrocopyKKLN<QNSRPEAPNWATQDSGF

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 25 .52 RPM
SRP017611_kidney 0 .00 RPM 39 .15 RPM
SRP017611_liver 0 .00 RPM 21 .45 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_1133 retrocopy.

TSS - click to see more details

Rattus norvegicus was not studied using FANTOM5 data.

Lab - click to see more details

retro_rnor_1133 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_rnor_1133 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 18 parental genes, and 27 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000067021 retrocopy
retro_btau_291,
Canis familiaris ENSCAFG000000007021 retrocopy
retro_cfam_1127,
Callithrix jacchus ENSCJAG000000064583 retrocopies
retro_cjac_2333, retro_cjac_2686, retro_cjac_701,
Equus caballus ENSECAG000000002361 retrocopy
retro_ecab_860,
Echinops telfairi ENSETEG000000131051 retrocopy
retro_etel_2048,
Felis catus ENSFCAG000000036651 retrocopy
retro_fcat_231,
Homo sapiens ENSG000001044081 retrocopy
retro_hsap_3489,
Gorilla gorilla ENSGGOG000000229552 retrocopies
retro_ggor_2354, retro_ggor_2355,
Myotis lucifugus ENSMLUG000000072691 retrocopy
retro_mluc_1796,
Macaca mulatta ENSMMUG000000113591 retrocopy
retro_mmul_2585,
Mustela putorius furoENSMPUG000000059242 retrocopies
retro_mputfur_193, retro_mputfur_736,
Mus musculus ENSMUSG000000223362 retrocopies
retro_mmus_1801, retro_mmus_2807,
Nomascus leucogenys ENSNLEG000000041201 retrocopy
retro_nleu_333,
Oryctolagus cuniculus ENSOCUG000000080501 retrocopy
retro_ocun_1399,
Pan troglodytes ENSPTRG000000205051 retrocopy
retro_ptro_2362,
Rattus norvegicus ENSRNOG00000027690 4 retrocopies
retro_rnor_1133 , retro_rnor_2879, retro_rnor_583, retro_rnor_584,
Ictidomys tridecemlineatus ENSSTOG000000089761 retrocopy
retro_itri_545,
Tursiops truncatus ENSTTRG000000110252 retrocopies
retro_ttru_1602, retro_ttru_1794,


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