RetrogeneDB ID: | retro_rnor_2285 | ||
Retrocopy location | Organism: | Rat (Rattus norvegicus) | |
| Coordinates: | 6:49062537..49063786(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Eif3b | ||
| Ensembl ID: | ENSRNOG00000001253 | ||
| Aliases: | Eif3b, Eif3s9 | ||
| Description: | Eukaryotic translation initiation factor 3 subunit B [Source:UniProtKB/Swiss-Prot;Acc:Q4G061] |
Retrocopy-Parental alignment summary:
>retro_rnor_2285
ACAGAGACATATGTGCACTGGTCCCCTAAGGGCACCTACCTGGCCACTTTTCATCAGAGGGGCATCACCTTCTGGGGAGG
GGACAAGTTCAAACAGATCCAGCTACCGAGGCATGCAGCTCATCAATTTCTCTCCTGTGAAAGATACCTGGTGGCTTTCA
GTCCACTGATGGACATTCAGGAAGACTCTCAGACCATTGTCATCTGAGACATCCTCACAGGTCATAAGAAGAGAGCCCTT
CATTGTGAATGCTGAGCCAACTGGCCCATCTTCAAGTTGAGTCACGATAACAAATTCTTTGCAGGAATGACCCTAGAAAC
TTTCAGCATCTATGAAACACCTTCTATGGGTCTTTTAGACAAGAAGAGCTTGAAGATCTCTGGAATAAAATCTTTTCTTA
ATCTCCGGGTGGTAACATCTTTGCCTTTTGGGTGCTGAAAGACAAAGATATTCCAGCCAGGGTGACGCTTATGCAGATAC
CCACTTGACAGGAGATCTGAGTGAGGAATTTGTTCAATGTGGTAGACAAGCTGCACTGGCAGAAACATGGAGATTACCTG
TTTCTAAAAGTGAACAGAACTCTGAAAGGCACACTGGGTGTTGTCACAACTTTTAAAATCTTCTGAATGAGGGAGAAGCA
GGCACCTGTTGATGTTCTTATGGTTTCTTTCATCTTATGGCCTTTGCCTGGGAACCCAACGGCAGTAAGTTTGCTGTACT
TCATGGTGAGGCCCCGCAGATATCTGTCTCCTTCTAGTATATGAAGGACAATGGGAAGATCAAACTCATCAAGATGTTTG
TCAAGCAGCAAACAAGCACCATCTTCTGGAGTACCCAGGGGCTTTCATGGTGCTGGCCTGGCTGAAGAGCAAGAGCCATG
CCTCAGTGTTTGTTGACACCTCAGATTGCATTGTCATGAACATTGCAGAGCAATACATGGCCTCTGATGTTGAGTGGGAC
CCAACCGAGCACTACATAGTGTCATGGTGGAGCCATAAGGTGGACAATACTTATTGGTTGTGGACCTTTCAAGATTGCTT
TCTCCAGAAAAACAACAAGGACCGTTTTTGCCAGCTGCTTTGGAGAACAAGGCCGGCAATGATCCTCAGCCAGGATAAGA
GAAAGCAAATTAAAAAGATCTGAAGAAATATTCTAAGATCTTTGAGCAAAAGGATCACTTGAGCCAGTCCAAAGCTTCAA
AGGGACTGTAGAAAGAAGTTGGATCATGATTGGGGACTTTCAGCAATAC
ORF - retro_rnor_2285 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 74.88 % |
| Parental protein coverage: | 53.32 % |
| Number of stop codons detected: | 7 |
| Number of frameshifts detected: | 5 |
Retrocopy - Parental Gene Alignment:
| Parental | TETYVRWSPKGTYLATFHQRGIALWGGDKFKQIQRFSHQGVQLIDFSPCERYLVTFSPLMDTQDDPQAII |
| TETYV.WSPKGTYLATFHQRGI..WGGDKFKQIQ...H...Q...F..CERYLV.FSPLMD.Q.D.Q.I. | |
| Retrocopy | TETYVHWSPKGTYLATFHQRGITFWGGDKFKQIQLPRHAAHQ---FLSCERYLVAFSPLMDIQEDSQTIV |
| Parental | IWDILTGHKKRGFHCESSAHWPIFKWSHDGKFFARMTLDTLSIYETPSMGLLDKKSLKISGIKD-FSWSP |
| I.DILTGHKKR..HCE..A.WPIFK.SHD.KFFA.MTL.T.SIYETPSMGLLDKKSLKISGIK..FS.SP | |
| Retrocopy | I*DILTGHKKRALHCEC*ANWPIFKLSHDNKFFAGMTLETFSIYETPSMGLLDKKSLKISGIKS<FS*SP |
| Parental | GGNIIAFWVPEDKDIPARVTLMQLPTRQEIRVRNLFNVVDCKLHWQKNGDYLCVKVDRTPKGTQGVVTNF |
| GGNI.AFWV..DKDIPARVTLMQ.PT.QEI.VRNLFNVVD.KLHWQK.GDYL..KV.RT.KGT.GVVT.F | |
| Retrocopy | GGNIFAFWVLKDKDIPARVTLMQIPT*QEI*VRNLFNVVD-KLHWQKHGDYLFLKVNRTLKGTLGVVTTF |
| Parental | EIFRMREKQVPVDVVEMKET-IIAFAWEPNGSKFAVLHGEAPRISVSFYHVKSNGKIELIKMFDKQQANT |
| .IF.MREKQ.PVDV.........AFAWEPNGSKFAVLHGEAP.ISVSF...K.NGKI.LIKMF.KQQ..T | |
| Retrocopy | KIF*MREKQAPVDVLMVSFI<LMAFAWEPNGSKFAVLHGEAPQISVSF*YMKDNGKIKLIKMFVKQQTST |
| Parental | IFWSPQ-GQFVVLAGLRSMNGALAFVDTSDCTVMNIAEHYMASDVEWDPTGRYVVTSVSWWSHKVDNAYW |
| IFWS.Q.G.F.VLA.L.S...A..FVDTSDC.VMNIAE.YMASDVEWDPT..Y.V...SWWSHKVDN.YW | |
| Retrocopy | IFWSTQ<GAFMVLAWLKSKSHASVFVDTSDCIVMNIAEQYMASDVEWDPTEHYIV---SWWSHKVDNTYW |
| Parental | LWTFQGRLLQKNNKDRFCQLLWRPRPPTLLSQDQIKQIK-KDLKKYSKIFEQKDRLSQSKASKEL-VERR |
| LWTFQ...LQKNNKDRFCQLLWR.RP...LSQD..KQIK.KDLKKYSKIFEQKD.LSQSKASK.L.VER. | |
| Retrocopy | LWTFQDCFLQKNNKDRFCQLLWRTRPAMILSQDKRKQIK<KDLKKYSKIFEQKDHLSQSKASKGL<VERS |
| Parental | RTMMEDFRQY |
| ..M..DF.QY | |
| Retrocopy | WIMIGDFQQY |
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 | 72 .62 RPM |
| SRP017611_kidney | 0 .00 RPM | 127 .14 RPM |
| SRP017611_liver | 0 .00 RPM | 54 .60 RPM |
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_2285 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_2285 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_rnor_2285 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Rattus norvegicus | ENSRNOG00000001253 | 1 retrocopy |
retro_rnor_2285 ,
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