RetrogeneDB ID: | retro_rnor_2322 | ||
Retrocopy location | Organism: | Rat (Rattus norvegicus) | |
| Coordinates: | 6:114989415..114990627(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Bckdk | ||
| Ensembl ID: | ENSRNOG00000019485 | ||
| Aliases: | None | ||
| Description: | [3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:Q00972] |
Retrocopy-Parental alignment summary:
>retro_rnor_2322
ATGATACTGACTTCAGTGCTGGGCAGCGGCCCTCGGAGCGGGTCTTAACTTTGGCCCCCTCTTAGGGTCCTCACTGTCAT
TCCGGGTTCGCTCAACATCAGCCACCGATACACACCATGTAGAGCTGGCCAGGGAACGCTCCAAGACTGTTACCTCCTTT
TACAACCAGTCAGCTATTGATGTGGTAGCAGAGAAGCCCTCAGTCTGCCTCACTCCCACCATGATGCTCTATTCTGGTCA
CTCACAGGATGGCAGCCACCTTCTGAAAAGTGGCTGCTACTTGCAGCAAGAGTTATCGGTGAGGATCGCTCACCGCATCA
AGGCCTTCCGTAGTCTTCCTTTCATCATTGGTTGCAACCCTACCATATTGCGTGTGCACGAGCTTTACGTCCGGGTCTTC
CAGAAGCTGACAGACTTCCCTCCGATCAAGGACCAGGCAGACTAGGCCCAGTATTGCCAGCTGGTGCGACAGCTGCTAGA
TGACCACAAGGATGTGGTGACCCTGTTAGCTGAGGGTCTTCGTGAGAGCCGGAAACACATAGAGGATGAAAAGCTAGTCT
GGTACTTGCTGGATAAAACACTAAAGTCCAGACTTGGGATCCGAATGCTGGCTACTCACCACTTGGCGCTACATGAAGAC
AAGCCTGATTTTGTTGGCATCATCTGCACTCGTCTGTCACCCAAGAAGATTATTGAGAAGTGGGTGGATTTTGCCAGATG
CCTGTGTGAGCACAAGTATGGCAATGCCCCTCGAGTCCGCATCAATGGGCATGTGGCTGCCGGTTTCCCCTTCATTCCTA
TGCGGCTGGACTATATCCTGCCTGAGCTCCTCAAGAACGCCGTGAGAGCCACAATGGGGAGTCACCTAGACACGCCCTAC
AATGTTCCTGATGTGGTCATCACCATCGCCAGTAATGTTGTGGATCTCATCATCAGGATCTCAGACCAGGGTGGAGGAAT
CGCTCATAATGACCTGGATCGAGTCATGGACCACCACTTCACCACATCTGAGGCCAGCACCCAGGACCCCCAAATCGGCC
CCCTCTTCGGCCACCTGGATATGCACAGTGGACCTATGCATGGCTTTGGCTTCCGGTTGCCTATGCGGAGTATCTCGTTG
GCTCCCTGCACCTGCAGTCCCTGCAGGGCATTGGCACAGATGTCTACCTACGGCTCTGCCACATTGATGGCCGGGAGGAA
AGCTTCAGAATC
ORF - retro_rnor_2322 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 90.1 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | MILTSVLGSGPRSGSSLWP-LLGSSLSLRVRSTSATDTHHVELARERSKTVTSFYNQSAIDVVAEKPSVR |
| MILTSVLGSGPRSGS.LWP.LLGSSLS.RVRSTSATDTHHVELARERSKTVTSFYNQSAIDVVAEKPSV. | |
| Retrocopy | MILTSVLGSGPRSGS*LWP>LLGSSLSFRVRSTSATDTHHVELARERSKTVTSFYNQSAIDVVAEKPSVC |
| Parental | LTPTMMLYSGRSQDGSHLLKSGRYLQQELPVRIAHRIKGFRSLPFIIGCNPTILHVHELYIRAFQKLTDF |
| LTPTMMLYSG.SQDGSHLLKSG.YLQQEL.VRIAHRIK.FRSLPFIIGCNPTIL.VHELY.R.FQKLTDF | |
| Retrocopy | LTPTMMLYSGHSQDGSHLLKSGCYLQQELSVRIAHRIKAFRSLPFIIGCNPTILRVHELYVRVFQKLTDF |
| Parental | PPIKDQADEAQYCQLVRQLLDDHKDVVTLLAEGLRESRKHIEDEKLVRYFLDKTLTSRLGIRMLATHHLA |
| PPIKDQAD.AQYCQLVRQLLDDHKDVVTLLAEGLRESRKHIEDEKLV.Y.LDKTL.SRLGIRMLATHHLA | |
| Retrocopy | PPIKDQAD*AQYCQLVRQLLDDHKDVVTLLAEGLRESRKHIEDEKLVWYLLDKTLKSRLGIRMLATHHLA |
| Parental | LHEDKPDFVGIICTRLSPKKIIEKWVDFARRLCEHKYGNAPRVRINGHVAARFPFIPMPLDYILPELLKN |
| LHEDKPDFVGIICTRLSPKKIIEKWVDFAR.LCEHKYGNAPRVRINGHVAA.FPFIPM.LDYILPELLKN | |
| Retrocopy | LHEDKPDFVGIICTRLSPKKIIEKWVDFARCLCEHKYGNAPRVRINGHVAAGFPFIPMRLDYILPELLKN |
| Parental | AMRATMESHLDTPYNVPDVVITIANNDVDLIIRISDRGGGIAHKDLDRVMDYHFTTAEASTQDPRISPLF |
| A.RATM.SHLDTPYNVPDVVITIA.N.VDLIIRISD.GGGIAH.DLDRVMD.HFTT.EASTQDP.I.PLF | |
| Retrocopy | AVRATMGSHLDTPYNVPDVVITIASNVVDLIIRISDQGGGIAHNDLDRVMDHHFTTSEASTQDPQIGPLF |
| Parental | GHLDMHSGGQSGPMHGFGFG-LPTSRAYAEYLGGSLQLQSLQGIGTDVYLRLRHIDGREESFRI |
| GHLDMH....SGPMH..GFG.LP...AYAEYL.GSL.LQSLQGIGTDVYLRL.HIDGREESFRI | |
| Retrocopy | GHLDMH----SGPMH--GFG<LPV--AYAEYLVGSLHLQSLQGIGTDVYLRLCHIDGREESFRI |
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 .22 RPM | 33 .07 RPM |
| SRP017611_kidney | 0 .07 RPM | 112 .56 RPM |
| SRP017611_liver | 0 .00 RPM | 22 .46 RPM |
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_2322 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_2322 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_rnor_2322 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Echinops telfairi | ENSETEG00000014497 | 1 retrocopy | |
| Monodelphis domestica | ENSMODG00000001837 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000019485 | 1 retrocopy |
retro_rnor_2322 ,
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