RetrogeneDB ID: | retro_rnor_456 | ||
Retrocopy location | Organism: | Rat (Rattus norvegicus) | |
| Coordinates: | 1:84514606..84516914(+) | ||
| Located in intron of: | ENSRNOG00000043320 | ||
Retrocopy information | Ensembl ID: | ENSRNOG00000046673 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Eif4g2 | ||
| Ensembl ID: | ENSRNOG00000017158 | ||
| Aliases: | None | ||
| Description: | eukaryotic translation initiation factor 4 gamma, 2 [Source:RefSeq peptide;Acc:NP_001017374] |
Retrocopy-Parental alignment summary:
>retro_rnor_456
GTGGAGAGTGCGATTGCAGAAGGGAGTGCTTCTCATTTCAGTGCTTCTTCGGGCAGAGGAGAAAGTAGGGGTGCACCTCA
GCACTATCCCAAGAATGCTGGCAACAGTGAGTTCCTGGGGAAAACCCCAGGGCAAAACTCTCAGAAATTGATTCCTGCAC
GAAGCACTAGACAAGATGACAACTCTACAGCAAACAGCTCCACAAATGAAATCTTCAGGATGCAATCTTCAGGAAAGTAA
GAGGCATAATAAATAAGCTTACTCCTGAAAAGTTTGACAAGCTATGCCTTGAGCTCCTCAATGTGGGTATAGAGTCTACA
TTCATCCTTAAATGGGTCATACTGCTGATTTTGCACAAAACCGTAGAAGAGCCAAAGCATAGCTCACTGTATGCTCAGCT
ATGTCTGTGATTGGCAGAAGATGCACCAAACTTTGATGGCCCAGCAGCAGAGGGTCAACCAGGACAGAAGCAAAGTACAA
CATTCAGACGCCTTTTGATTTCCAAATTGTAAGATGAATTTGAAAACCGAACTAGAAATGTTGATGTCTATGATAAGCAT
GAAAATCCCCTCCTCCCTGAGGAGGAGGAACAGAGAGCCATTGCTAAGATCAAGATGTTGGAGAACATCAAATTCATTGG
AGATCTTGGCAAGCTTGAACTTATTCATGAATGTATCCTTCATAAGTGCATCAAAACACTTTTGGAAAAGAAGAGAGTCC
AATTCAAAGATATGGGAGAGGATTTGGAGTGCCTCTGTCAGATAATGAGGACAGTGGGACCTCTATTAGACCATGAACGA
GCCAAGTCCTTAATGGATCAGTACTTGGCCCAGAATGTGTTCCCTTAATGTTAAGTAAGGAATTGCCATCCAGGATTCAT
TTCCTACTGCAGGATACTGTAGAGTTGCAAGAGCACCATTGGGTTTCTCGCAAGGCTTTTCTTGACAATGGACCAAAGAC
GATCAGTCAAATCCGTCAAGATGCAGTAAAAGATCTAGGAGTGTTTATTTCTGCTCCTATGGCTCAAGGGAGGAATGACT
TCTTCCTGGAGGGACTGTCCATGCTGCCAATGATGAAAATGGATAGGGACCCACTTGGGGGACTCGCCGATATGTTTGGA
CAAATGCCAGGTAGTGGAATTGGTACTGGTCCAGGAGTTATCCAGGATAGATTTTCACCTACAATGGGATGTCATCGTTC
AAATCAGCTCTTCAATGGCCATGGGGAACATATCATGCCTCCCACGCAATCGCAGTTGGAGAGATGGGGGGGGGGCAAGT
TTATGAAAAGCCAGGGGCTAAGCCAGTTCTACCATAACCAGAGTCAGGGACTCTTATCCCAGCTGCAAGGACAGTCGAAG
GATATGCCACCTTGGTTTTCTAAGAAAGGACAGCTTAATGCAGCTGAGATTAGTTTGAGGCCTGCTCAGTCGTTTCTAAT
GAATAAAAATCAGGTGCCAAAGCTTCATCTCCAGATAACTATGATTCCTCCCAGTGCACAGCCACCACGCACTCAAACAC
CACCTGTGGGACAGACACCTCAACTTGGTCTCAAAACTAATCCACCACTTATCCAGGAAAAGACTGCCAAGACTAGCAAA
GAACCACCACCATCAAAGGAAGAACTACTTAAACTGACCGAAGCTGTTTTAACTGAGTATCTGAACAGTGGAAATGCCAA
TAATGCTGTCAGTGGTGTGAGAGAAATGAGAGCTCCAAAACACTTTCTTCCTGAGATGTTAAGCAAAGTGAGCATCCTGT
CACTTGATAGAAGTGATGAAGTTAAAGAAAAAGCAAGCTCTTTGATCAATTTACTCAAACAGGAAGGGATAGCCGCAAGT
GACAACTTTATGCAGGTTTTCCTGAATGTATTGGAGCAGTGTCCCAAACTGGAGGTTGACATCCCCTTGGTGAAATCTTA
CTTGGCACAATTTATGGCTCGTGCTATAATTTCAGATTTGGTCAGCATTTCAGAACTAGCTCAACCACTGGAGAGTGGCA
CCCACTTCCCTCTCTTCTTATTTTGTCTTCAACAATTAGCTAAATTACAAGCCCAAGAATGGTTAGCTGAACTTTTTAAA
CAAAGCAAGGTCAATATGCAGAAAATGCTGCCAGAAAATGATCAGAATAAGGATCAAATGTTGGAGATTTTGGAAGGAAA
GGGACTGAGTTTCTTATTCCCACTCCTTAAATTGGAGAAGAAACTATTGAAGCAAATTAAGCTGGATCCATCCCCTCAAA
CTATATATAAATGGATTAAAGATAACATCTCTCCCAAACTTCATGTAGATAAAGGATTTGTGAACATC
ORF - retro_rnor_456 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 87.86 % |
| Parental protein coverage: | 84.99 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | VESAIAEGGASRFSASSGGGGSRGAPQHYPKTAGNSEFLGKTPGQNAQKWIPARSTRRDDNSAANNSANE |
| VESAIAEG.AS.FSASSG.G.SRGAPQHYPK.AGNSEFLGKTPGQN.QK.IPARSTR..D.....NS... | |
| Retrocopy | VESAIAEGSASHFSASSGRGESRGAPQHYPKNAGNSEFLGKTPGQNSQKLIPARSTRQ-DDNSTANSSTX |
| Parental | KERHDAIFRK-VRGILNKLTPEKFDKLCLELLNVGVESKLILKGVILLIVDKALEEPKYSSLYAQLCLRL |
| .........K.VRGI.NKLTPEKFDKLCLELLNVG.ES..ILK.VILLI..K..EEPK.SSLYAQLCL.L | |
| Retrocopy | XXXXXXXXXK<VRGIINKLTPEKFDKLCLELLNVGIESTFILKWVILLILHKTVEEPKHSSLYAQLCL*L |
| Parental | AEDAPNFDGPAAEGQPGQKQSTTFRRLLISKLQDEFENRTRNVDVYDKRENPLLPEEEEQRAIAKIKMLG |
| AEDAPNFDGPAAEGQPGQKQSTTFRRLLISKL.DEFENRTRNVDVYDK.ENPLLPEEEEQRAIAKIKML. | |
| Retrocopy | AEDAPNFDGPAAEGQPGQKQSTTFRRLLISKL*DEFENRTRNVDVYDKHENPLLPEEEEQRAIAKIKMLE |
| Parental | NIKFIGELGKLDLIHESILHKCIKTLLEKKKRVQLKDMGEDLECLCQIMRTVGPRLDHERAKSLMDQYFA |
| NIKFIG.LGKL.LIHE.ILHKCIKTLLEKK.RVQ.KDMGEDLECLCQIMRTVGP.LDHERAKSLMDQY.A | |
| Retrocopy | NIKFIGDLGKLELIHECILHKCIKTLLEKK-RVQFKDMGEDLECLCQIMRTVGPLLDHERAKSLMDQYLA |
| Parental | -RMCSL-MLSKELPARIRFLLQDTVELREHHWVPRKAFLDNGPKTINQIRQDAVKDLGVFIPAPMAQGRN |
| .RMCSL.MLSKELP.RI.FLLQDTVEL.EHHWV.RKAFLDNGPKTI.QIRQDAVKDLGVFI.APMAQGRN | |
| Retrocopy | >RMCSL>MLSKELPSRIHFLLQDTVELQEHHWVSRKAFLDNGPKTISQIRQDAVKDLGVFISAPMAQGRN |
| Parental | DFFLEGPFMPPRMKMDRDPLGGLADMFGQMPGSGIGTGPGVIQDRFSPTMGRHRSNQLFNGHGGHIMPPT |
| DFFLEG..M.P.MKMDRDPLGGLADMFGQMPGSGIGTGPGVIQDRFSPTMG.HRSNQLFNGHG.HIMPPT | |
| Retrocopy | DFFLEGLSMLPMMKMDRDPLGGLADMFGQMPGSGIGTGPGVIQDRFSPTMGCHRSNQLFNGHGEHIMPPT |
| Parental | QSQFGEMGG-KFMKSQGLSQLYHNQSQGLLSQLQGQSKDMPPRFSKKGQLNADEISLRPAQSFLMNKNQV |
| QSQ.......KFMKSQGLSQ.YHNQSQGLLSQLQGQSKDMPP.FSKKGQLNA.EISLRPAQSFLMNKNQV | |
| Retrocopy | QSQLERXXXXKFMKSQGLSQFYHNQSQGLLSQLQGQSKDMPPWFSKKGQLNAAEISLRPAQSFLMNKNQV |
| Parental | PKLQPQITMIPPSAQPPRTQTPPLGQTPQLGLKTNPPLIQEKPAKTSKKPPPSKEELLKLTEAVVTEYLN |
| PKL..QITMIPPSAQPPRTQTPP.GQTPQLGLKTNPPLIQEK.AKTSK.PPPSKEELLKLTEAV.TEYLN | |
| Retrocopy | PKLHLQITMIPPSAQPPRTQTPPVGQTPQLGLKTNPPLIQEKTAKTSKEPPPSKEELLKLTEAVLTEYLN |
| Parental | SGNANDAVSGVREMRAPKHFLPEMLSKVIILSLDRSDEDKEKASSLISLLKQEGIATSDNFMQAFLNVLE |
| SGNAN.AVSGVREMRAPKHFLPEMLSKV.ILSLDRSDE.KEKASSLI.LLKQEGIA.SDNFMQ.FLNVLE | |
| Retrocopy | SGNANNAVSGVREMRAPKHFLPEMLSKVSILSLDRSDEVKEKASSLINLLKQEGIAASDNFMQVFLNVLE |
| Parental | QCPKLEVDIPLVKSYLAQFAARAIISELVSISELAQPLESGTHFPLFLLCLQQLAKLQDREWLTELFQQS |
| QCPKLEVDIPLVKSYLAQF.ARAIIS.LVSISELAQPLESGTHFPLFL.CLQQLAKLQ..EWL.ELF.QS | |
| Retrocopy | QCPKLEVDIPLVKSYLAQFMARAIISDLVSISELAQPLESGTHFPLFLFCLQQLAKLQAQEWLAELFKQS |
| Parental | KVNMQKMLPEIDQNKDRMLEILEGKGLSFLFPLLKLEKELLKQIKLDPSPQTIYKWIKDNISPKLHVDKG |
| KVNMQKMLPE.DQNKD.MLEILEGKGLSFLFPLLKLEK.LLKQIKLDPSPQTIYKWIKDNISPKLHVDKG | |
| Retrocopy | KVNMQKMLPENDQNKDQMLEILEGKGLSFLFPLLKLEKKLLKQIKLDPSPQTIYKWIKDNISPKLHVDKG |
| Parental | FVNI |
| FVNI | |
| Retrocopy | FVNI |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
(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 | 350 .85 RPM |
| SRP017611_kidney | 0 .14 RPM | 880 .93 RPM |
| SRP017611_liver | 0 .13 RPM | 298 .40 RPM |
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_456 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_456 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_rnor_456 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000020308 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000001738 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000017158 | 2 retrocopies |
retro_rnor_2674, retro_rnor_456 ,
|