RetrogeneDB ID:

retro_rnor_287

Retrocopy
location
Organism:Rat (Rattus norvegicus)
Coordinates:2:247895382..247896474(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSRNOG00000009835
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:Tram1
Ensembl ID:ENSRNOG00000007892
Aliases:None
Description:Translocating chain-associated membrane protein 1 [Source:UniProtKB/Swiss-Prot;Acc:Q5XI41]


Retrocopy-Parental alignment summary:






>retro_rnor_287
ATGGGGCTCCGCAAGAAGAACGCCAGGAACCCCCCGGTGCTGAGCCACGAATTCATGGTGCAGAACCACGCGGATATGGT
CTCCTGCGTGGGCATGTTCTTCGTGCTGGGACTTATGTTCGAGGGCACGGCCGAGATGTCGATCGTGTTCCTCACCCTGC
AGCATGGAGTCGTTGTCCCAGCGGAAGGGCTACCCTCGGGGTCCAGGACCCTTTACCATTATGGGGTCAAAGATCTGGCC
ACAGTGTTCTTCTACATGCTGGTGGCCATCATCATTCACGCCACCATTCAGGAGTACGTGCTAGATAAGCTCAGCCGGAG
ACTGCAGCTCACCAAAGGCAAACAAAACAAATTGAATGAGGCCGGGCAGCTGAGTGTGTTCTACATAGTGTCTGGTATCT
GGGGTATGATCATTCTGGCCTCTGAGAACTGCCTGTCAGACCCCACTCTATTGTGGAAGTCTCAGCCCCACAACATGATG
ACATTTCAGATGAAATTTTTCTACATCTCACAGTTGGCTTACTGGTTTCATAGTTTCCCGGAGCTCTACTTCCAGAAAGT
CAGGAAACAAGATATCCCGGGTCAACTCATCTACATTGGCCTCCACCTCTTCCACATTGGAGGGGCCTATCTCTTGTACT
TGAACCACCTGGGCCTGCTGCTTCTGATGCTGCACTATGCTGTCGAGCTCCTCTCCAGCGTGTGCAGCCTGCTTTACTTT
GGCGATGAGCGGTACCAGAAAGGGTTGTCTTTGTGGCCTATCGTGTTTATATCCGGGAGACTCGTGACACTGATTGTCTC
AGTGGTTACAGTAGGGCTTCACTTGGCCGGGACAAATCGGAATGGAAATGCTCTCTCTGGTAATGTCAATGTGTTGGCAG
CTAAAATCGCTGTTCTGTCCTCGAGTTGCAGTATCCAGGTGTACATAACATGGACCTTGACGACCGTCTGGCTTCAGAGA
TGGTTAGAAGATGCGAATCTTCATGTCTGTGGGAGGAAGAGACGGTCCAGGTCGAGAAAAGGCACAGAAAATGGAGTGGA
GAATCCAAATAGAATAGATTCTCCACCAAAGAAGAAAGAGAAAGCTCCTTAG

ORF - retro_rnor_287 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 59.09 %
Parental protein coverage: 94.12 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMAIRKKSNKNPPVLSHEFVLQNHADIVSCLAMLFLLGLMFEITAKGAIIFVALQYNVTRPATEEQAAESA
M..RKK...NPPVLSHEF..QNHAD.VSC..M.F.LGLMFE.TA...I.F..LQ..V..PA.E.....S.
RetrocopyMGLRKKNARNPPVLSHEFMVQNHADMVSCVGMFFVLGLMFEGTAEMSIVFLTLQHGVVVPA-EGLPSGSR
ParentalSLYYYGIKDLATVFFYMLVAIIVHAIIQEYVLDKINRRMHFSKTKHSKFNESGQLSAFYLFACVWGTFIL
.LY.YG.KDLATVFFYMLVAII.HA.IQEYVLDK..RR....K.K..K.NE.GQLS.FY.....WG..IL
RetrocopyTLYHYGVKDLATVFFYMLVAIIIHATIQEYVLDKLSRRLQLTKGKQNKLNEAGQLSVFYIVSGIWGMIIL
ParentalVSENYISDPTILWRAYPHNLMTFQMKFFYISQLAYWLHAFPELYFQKTKKEDIPRQLVYIGLYLFHIAGA
.SEN..SDPT.LW...PHN.MTFQMKFFYISQLAYW.H.FPELYFQK..K.DIP.QL.YIGL.LFHI.GA
RetrocopyASENCLSDPTLLWKSQPHNMMTFQMKFFYISQLAYWFHSFPELYFQKVRKQDIPGQLIYIGLHLFHIGGA
ParentalYLLNLNHLGLVLLVLHYFVEFLFHISRLFYFSDEKYQKGFSLWAVLFVLGRLLTLILSVLTVGFGLARAE
YLL.LNHLGL.LL.LHY.VE.L.....L.YF.DE.YQKG.SLW...F..GRL.TLI.SV.TVG..LA...
RetrocopyYLLYLNHLGLLLLMLHYAVELLSSVCSLLYFGDERYQKGLSLWPIVFISGRLVTLIVSVVTVGLHLA-GT
ParentalNQKLDFSTGNFNVLAVRIAVLASICITQAFMMWKFINFQLRRWREHSAFQAPPVKRKPAVTKGRSSRKGT
N.......GN.NVLA..IAVL.S.C..Q....W......L.RW.E.........KR.....KG.....G.
RetrocopyNRNGNALSGNVNVLAAKIAVLSSSCSIQVYITWTLTTVWLQRWLEDANLHVCGRKRRSRSRKG--TENGV
ParentalEN
EN
RetrocopyEN

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 15 .67 RPM 41 .20 RPM
SRP017611_kidney 0 .21 RPM 157 .29 RPM
SRP017611_liver 1 .14 RPM 373 .57 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_287 retrocopy.

TSS - click to see more details

Rattus norvegicus was not studied using FANTOM5 data.

Lab - click to see more details

retro_rnor_287 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_rnor_287 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 25 parental genes, and 26 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000063251 retrocopy
retro_amel_78,
Bos taurus ENSBTAG000000075621 retrocopy
retro_btau_24,
Canis familiaris ENSCAFG000000078661 retrocopy
retro_cfam_15,
Callithrix jacchus ENSCJAG000000078931 retrocopy
retro_cjac_168,
Dasypus novemcinctus ENSDNOG000000092962 retrocopies
retro_dnov_27, retro_dnov_906,
Dipodomys ordii ENSDORG000000019011 retrocopy
retro_dord_27,
Equus caballus ENSECAG000000183781 retrocopy
retro_ecab_506,
Echinops telfairi ENSETEG000000184471 retrocopy
retro_etel_674,
Felis catus ENSFCAG000000287751 retrocopy
retro_fcat_136,
Homo sapiens ENSG000000671671 retrocopy
retro_hsap_51,
Loxodonta africana ENSLAFG000000116251 retrocopy
retro_lafr_9,
Macaca mulatta ENSMMUG000000015161 retrocopy
retro_mmul_235,
Monodelphis domestica ENSMODG000000073161 retrocopy
retro_mdom_308,
Mustela putorius furoENSMPUG000000106161 retrocopy
retro_mputfur_558,
Mus musculus ENSMUSG000000259351 retrocopy
retro_mmus_117,
Nomascus leucogenys ENSNLEG000000113761 retrocopy
retro_nleu_73,
Oryctolagus cuniculus ENSOCUG000000087341 retrocopy
retro_ocun_52,
Otolemur garnettii ENSOGAG000000063791 retrocopy
retro_ogar_2932,
Pongo abelii ENSPPYG000000186601 retrocopy
retro_pabe_169,
Pan troglodytes ENSPTRG000000203341 retrocopy
retro_ptro_2081,
Rattus norvegicus ENSRNOG00000007892 1 retrocopy
retro_rnor_287 ,
Sus scrofa ENSSSCG000000061931 retrocopy
retro_sscr_980,
Ictidomys tridecemlineatus ENSSTOG000000055371 retrocopy
retro_itri_38,
Tarsius syrichta ENSTSYG000000138871 retrocopy
retro_tsyr_24,
Tursiops truncatus ENSTTRG000000003281 retrocopy
retro_ttru_24,




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