RetrogeneDB ID: | retro_rnor_1920 | ||
Retrocopy location | Organism: | Rat (Rattus norvegicus) | |
| Coordinates: | 3:131316577..131317313(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Chkb | ||
| Ensembl ID: | ENSRNOG00000011404 | ||
| Aliases: | Chkb, Chetk, Chkl | ||
| Description: | Choline/ethanolamine kinase [Source:UniProtKB/Swiss-Prot;Acc:O54783] |
Retrocopy-Parental alignment summary:
>retro_rnor_1920
TGGGTACAGAGCCGGCCATTGAAAACTCAAGAGCTCTAGGACCCAGTGTTGTTAGGAGCCATTGCAACAAAGATGGCCCG
TTTCCATAGTATGGAGATGCCCTTCACTAAGGAGCCCTGCTGGTTGTTTGGGACCATGGACCCGTACCTAAAGCAGATCC
AGGACCTGCCTTCCACTAGCCTTCCCCAGACGAACCTGGTGGAAATGTACAACCTCAAGGATGAGATGAACAACCTCAGG
AAGTTACTAGATGCTACACTGTCACCAGTGGTCTTCTGCCACAGTGACATACAGGAAGGAAACATCTTATTGCTCTCAGA
GCCAGACAGTGATGACAACCTCATGTTGGTTGATTTTGAGTACAGTAGTTACAAATGACTTTGACATTGGGAATCATTTC
TGTGAGTGGGTTTATGGTTATACTTACGAGGAATGGCCTTTCTACAAAGCAAGACCCACAGACTACCTCACTAGAGAACA
GCAACCCCGTTTCATCTGTCATTATCTAGCAGAGGTTCAGAAAGGTGAGGTCCTCTCCAAAGAGGAGCAGAAGAAACAGG
AAGACTTGCTGATAGAGATCAGCCGGTATGCCCTGGTGTCTCATTTCTTCTGGGGCCTATGGTCCACCCTCCAGGTTTCC
ATGTCCACCATAGAGTTTGGCTACGTGGAGTATGCCCAATCTTAGTTCCAGCTCTCCTTCCAGCAGAAGGGGCAGCTGAC
CAGTTTCCCATCACCG
ORF - retro_rnor_1920 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 83.53 % |
| Parental protein coverage: | 62.94 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | YLPSRPLKTQELRDPVLSGAIATKMARFHGMEMPFTKEPRWLFGTMERYLKQIQDLPSTSLPQMNLVEMY |
| ...SRPLKTQEL.DPVL.GAIATKMARFH.MEMPFTKEP.WLFGTM..YLKQIQDLPSTSLPQ.NLVEMY | |
| Retrocopy | WVQSRPLKTQEL*DPVLLGAIATKMARFHSMEMPFTKEPCWLFGTMDPYLKQIQDLPSTSLPQTNLVEMY |
| Parental | SLKDEMNHLRTLLDATPSPVVFCHNDIQEGNILLLSEPDSDDNLMLVDFEYSSYNYR-GFDIGNHFCEWV |
| .LKDEMN.LR.LLDAT.SPVVFCH.DIQEGNILLLSEPDSDDNLMLV........Y...FDIGNHFCEWV | |
| Retrocopy | NLKDEMNNLRKLLDATLSPVVFCHSDIQEGNILLLSEPDSDDNLMLV--DFEYSSYK>DFDIGNHFCEWV |
| Parental | YDYTYEEWPFYKARPADYPTREQQLLFIRHYLAEVQKGEVLSEEEQKKQEEDLLIEISRYALASHFFWGL |
| Y.YTYEEWPFYKARP.DY.TREQQ..FI.HYLAEVQKGEVLS.EEQKKQ.EDLLIEISRYAL.SHFFWGL | |
| Retrocopy | YGYTYEEWPFYKARPTDYLTREQQPRFICHYLAEVQKGEVLSKEEQKKQ-EDLLIEISRYALVSHFFWGL |
| Parental | WSTLQASMSTIEFGYLEYAQSRFQFYFQQKGQLTSFLSP |
| WSTLQ.SMSTIEFGY.EYAQS.FQ..FQQKGQLTSF.SP | |
| Retrocopy | WSTLQVSMSTIEFGYVEYAQS*FQLSFQQKGQLTSFPSP |
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 | 24 .37 RPM |
| SRP017611_kidney | 0 .00 RPM | 23 .31 RPM |
| SRP017611_liver | 0 .00 RPM | 25 .89 RPM |
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_1920 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_1920 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_rnor_1920 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Rattus norvegicus | ENSRNOG00000011404 | 2 retrocopies |
retro_rnor_1919, retro_rnor_1920 ,
|
| Tupaia belangeri | ENSTBEG00000000172 | 1 retrocopy |