RetrogeneDB ID: | retro_rnor_2674 | ||
Retrocopy location | Organism: | Rat (Rattus norvegicus) | |
| Coordinates: | 9:35862050..35863757(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSRNOG00000011124 | |
| 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_2674
GTGGAGAGTGCGATTGCAGAAGGGGGTGCTTCTCGTTTCAGTGCTTCTTCGGCGGAGGAGGAAGTAGGGGTGCACCTCAG
CACTATCCCAAGACTGCTGGCAACAGCGAGTTCCTGGGGAAAACCCCAGGGCAAAACGCTCAGAAATGGATTCCTGCACG
AAGCACTAGACGAGATGACAACTCCGCAGCAAACAACTCCGCAAATGAAAAAGAACGACATGATGCAATCTTCAGGAAAG
TAAGAGGCATACTAAATAAGCTTACTCCTGAAAAGTTTGACAAGCTATGCCTTGAGCTCCTCAATGTGGGTGTAGAGTCT
AAACTCATCCTTAAAGGGGTCATACTGCTGATTGTGGACAAAGCCCTAGAAGAGCCAAAGTATAGCTCACTGTATGCTCA
GCTATGTCTGCGATTGGCAGAAGATGCACCAAACTTTGATGGCCCAGCAGCAGAGGGTCAACCAGGACAGAAGCAAAGCA
CAACATTCAGACGCCTCTTGATTTCCAAATTGCAAGATGAATTTGAAAACCGAACCAGAAATGTTGATGTCTATGATAAG
CGTGAAAATCCCCTCCTCCCTGAGGAGGAGGAACAGAGAGCCATTGCTAAGATCAAGATGTTGGGGAACATCAAATTCAT
TGGAGAACTTGGCAAGCTTGATCTTATTCATGAATCTATCCTTCATAAGTGCATCAAAACACTTTTGGAAAAGAAGAAGA
GAGTCCAACTCAAAGATATGGGAGAGGATTTGGAGTGCCTCTGTCAGATAATGAGGACAGTGGGACCTCGATTAGACCAT
GAACGAGCCAAGTCCTTAATGGATCAGTACTTTGCCAGAATGTGTTCCTTAATGTTAAGTAAGGAATTGCCAGCCAGGAT
TCGTTTCCTACTGCAGGATACCGTAGAGTTGCGAGAGCACCATTGGGTTCCTCTCAAGGCTTTTCTTGACAATGGACCAA
AGACGATCAATCAAATCCGTCAAGATGCAGTAAAAGATCTAGGAGTGTTTATTCCTGCTCCTATGGCTCAAGGGAGGAAT
GACTTCTTCCTGGAGGGACCGTTCATGCCGCCAAGGATGAAAATGGATAGGGACCCACTTGGGGGACTCACTGATATGTT
TGGACAAATGCCAGGTAGTGGAATTGGTACTGGTCCAGGAGTTATCCAGGATAGATTTTCACCCACAATGGGACGTCATC
ATTCAAATCAGCTCTTCAATGGCCATGGGGGACACATCATGCCTCCCACGCAATCGCAGTTTGGAGAGATGGGGGGGCAA
GTTTATGAAAAGCCAGGGGCTAAGCCAGCTCTACCATAACCAGAGTCAGGGACTCTTATCCCAGCTGCAAGGACAGTCGA
AGGATATGCCACCTCGGTTTTCTAAGAAAGGACAGCTTAATGCAGATGAGATTAGTTTGAGGCCTGCTCAGTCGTTTCTA
ATGAATAAAAATCAGGTGCCAAAGCTTCAGCCCCAGATAACTATGATTCCTCCCAGTGCACAGCCACCACGCACTCAAAC
ACCACCTCTGGGACAGACACCTCAACTTGGTCTCAAAACTAATCCACCACTTATTCAGGAAAAGCCTGCCAAGACTAGCA
AAAAGCCACCACCATCAAAGGAAGAACTACTTAAACTGACCGAAGCTGTTGTAACTGAGTATCTGAACAGTGGAAATGCC
AACGACACGCTGTCAGTGGTGTGAGAG
ORF - retro_rnor_2674 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 98.42 % |
| Parental protein coverage: | 62.8 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | VESAIAEGGASRFSASS-GGGGSRGAPQHYPKTAGNSEFLGKTPGQNAQKWIPARSTRRDDNSAANNSAN |
| VESAIAEGGASRFSASS.GGGGSRGAPQHYPKTAGNSEFLGKTPGQNAQKWIPARSTRRDDNSAANNSAN | |
| Retrocopy | VESAIAEGGASRFSASS<GGGGSRGAPQHYPKTAGNSEFLGKTPGQNAQKWIPARSTRRDDNSAANNSAN |
| Parental | EKERHDAIFRKVRGILNKLTPEKFDKLCLELLNVGVESKLILKGVILLIVDKALEEPKYSSLYAQLCLRL |
| EKERHDAIFRKVRGILNKLTPEKFDKLCLELLNVGVESKLILKGVILLIVDKALEEPKYSSLYAQLCLRL | |
| Retrocopy | EKERHDAIFRKVRGILNKLTPEKFDKLCLELLNVGVESKLILKGVILLIVDKALEEPKYSSLYAQLCLRL |
| Parental | AEDAPNFDGPAAEGQPGQKQSTTFRRLLISKLQDEFENRTRNVDVYDKRENPLLPEEEEQRAIAKIKMLG |
| AEDAPNFDGPAAEGQPGQKQSTTFRRLLISKLQDEFENRTRNVDVYDKRENPLLPEEEEQRAIAKIKMLG | |
| Retrocopy | AEDAPNFDGPAAEGQPGQKQSTTFRRLLISKLQDEFENRTRNVDVYDKRENPLLPEEEEQRAIAKIKMLG |
| Parental | NIKFIGELGKLDLIHESILHKCIKTLLEKKKRVQLKDMGEDLECLCQIMRTVGPRLDHERAKSLMDQYFA |
| NIKFIGELGKLDLIHESILHKCIKTLLEKKKRVQLKDMGEDLECLCQIMRTVGPRLDHERAKSLMDQYFA | |
| Retrocopy | NIKFIGELGKLDLIHESILHKCIKTLLEKKKRVQLKDMGEDLECLCQIMRTVGPRLDHERAKSLMDQYFA |
| Parental | RMCSLMLSKELPARIRFLLQDTVELREHHWVPRKAFLDNGPKTINQIRQDAVKDLGVFIPAPMAQGRNDF |
| RMCSLMLSKELPARIRFLLQDTVELREHHWVP.KAFLDNGPKTINQIRQDAVKDLGVFIPAPMAQGRNDF | |
| Retrocopy | RMCSLMLSKELPARIRFLLQDTVELREHHWVPLKAFLDNGPKTINQIRQDAVKDLGVFIPAPMAQGRNDF |
| Parental | FLEGPFMPPRMKMDRDPLGGLADMFGQMPGSGIGTGPGVIQDRFSPTMGRHRSNQLFNGHGGHIMPPTQS |
| FLEGPFMPPRMKMDRDPLGGL.DMFGQMPGSGIGTGPGVIQDRFSPTMGRH.SNQLFNGHGGHIMPPTQS | |
| Retrocopy | FLEGPFMPPRMKMDRDPLGGLTDMFGQMPGSGIGTGPGVIQDRFSPTMGRHHSNQLFNGHGGHIMPPTQS |
| Parental | QFGEM-GGKFMKSQGLSQLYHNQSQGLLSQLQGQSKDMPPRFSKKGQLNADEISLRPAQSFLMNKNQVPK |
| QFGEM.GGKFMKSQGLSQLYHNQSQGLLSQLQGQSKDMPPRFSKKGQLNADEISLRPAQSFLMNKNQVPK | |
| Retrocopy | QFGEM>GGKFMKSQGLSQLYHNQSQGLLSQLQGQSKDMPPRFSKKGQLNADEISLRPAQSFLMNKNQVPK |
| Parental | LQPQITMIPPSAQPPRTQTPPLGQTPQLGLKTNPPLIQEKPAKTSKKPPPSKEELLKLTEAVVTEYLNSG |
| LQPQITMIPPSAQPPRTQTPPLGQTPQLGLKTNPPLIQEKPAKTSKKPPPSKEELLKLTEAVVTEYLNSG | |
| Retrocopy | LQPQITMIPPSAQPPRTQTPPLGQTPQLGLKTNPPLIQEKPAKTSKKPPPSKEELLKLTEAVVTEYLNSG |
| Parental | NANDAVSGVRE |
| NAND..S.V.E | |
| Retrocopy | NANDTLSVV*E |
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 .79 RPM | 350 .85 RPM |
| SRP017611_kidney | 1 .40 RPM | 880 .93 RPM |
| SRP017611_liver | 0 .47 RPM | 298 .40 RPM |
Rattus norvegicus was not studied using ChIP-Seq data.
13 EST(s) were mapped to retro_rnor_2674 retrocopy
| EST ID | Start | End | Identity | Match | Mis-match | Score |
|---|---|---|---|---|---|---|
| BF564540 | 35862128 | 35862541 | 100 | 412 | 0 | 411 |
| CB576038 | 35862148 | 35862785 | 100 | 637 | 0 | 637 |
| CB704586 | 35862619 | 35862956 | 100 | 337 | 0 | 337 |
| CB710016 | 35862547 | 35862827 | 100 | 280 | 0 | 280 |
| CB733125 | 35862228 | 35862687 | 100 | 459 | 0 | 459 |
| CB790699 | 35862183 | 35862620 | 100 | 437 | 0 | 437 |
| CB802190 | 35862295 | 35862695 | 100 | 400 | 0 | 400 |
| CB804519 | 35862410 | 35862792 | 99 | 377 | 0 | 374 |
| CB811688 | 35862265 | 35862654 | 99.3 | 382 | 2 | 374 |
| CO405723 | 35862250 | 35863007 | 99.5 | 729 | 2 | 718 |
| FM048541 | 35862469 | 35862902 | 100 | 433 | 0 | 433 |
| FQ108482 | 35862135 | 35862926 | 100 | 790 | 0 | 790 |
| FQ131574 | 35862224 | 35862954 | 99.9 | 729 | 1 | 728 |
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_2674 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_rnor_2674 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,
|