RetrogeneDB ID: | retro_rnor_1433 | ||
Retrocopy location | Organism: | Rat (Rattus norvegicus) | |
| Coordinates: | 19:48752201..48752858(+) | ||
| Located in intron of: | ENSRNOG00000019290 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Camk1d | ||
| Ensembl ID: | ENSRNOG00000017882 | ||
| Aliases: | Camk1d, RGD1560691 | ||
| Description: | calcium/calmodulin-dependent protein kinase type 1D [Source:RefSeq peptide;Acc:NP_001100835] |
Retrocopy-Parental alignment summary:
>retro_rnor_1433
TATGATATAAAGGCCCTGATTGGGCGAGGCAGCTTTAGCCGAGTGGTACGTGTGGAGCATCGGGCAACCCGACAGCCATA
TGCTATCAAGATGATTGAAACCAAGTACCGAGAAGGGCGGGAGGTGTGTGAGTCTGAGCTCCGAGTGCTGCGCCGGGTGC
GACACGCCAACATCATCCAGCTGGTAGAAGTGTTTGAGACACAGGAACGGGTATATATGGTAATGGAGCTGGCCACTGGT
GGTGAGCTCTTTGACCGGATTATTGCCAAGGGTTCTTTCACTGAGCGGGATGCCACAAGAGTGCTGCAAATGGTACTGGA
TGGTGTCCGGTATCTGCATGCCCTTGGCATCACACACCGAGACCTCAAGCCTGAGAATCTCCTTTACTATCACCCAGGCA
CTGACTCCAAGATCATCATCACTGACTTTGGCTTGGCCAGTGCCCGAAAGAAAGGTGATGACTGCCTGATGAAGACCACC
TGTGGCACACCTGAGTACATTGCTCCTGAGGTTCTGGTTCGGAAACCCTACACCAATTCTGTGGATATGTGGGCGCTGGG
TGTCATTGCCTACATCCTGCTCAGTGGCACCATGCCTTTTGAGGATGACAACCGCACCCGGCTATACCGGCAGATCCTCA
GGGGCAAATACAGTTAT
ORF - retro_rnor_1433 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 50.91 % |
| Parental protein coverage: | 56.92 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | FEFKETLGTGAFSEVVLAEEKATGKLFAVKCIPKKALKGKESSIENEIAVLRKIKHENIVALEDIYESPN |
| ...K...G.G.FS.VV..E..AT....A.K.I..K...G.E...E.E..VLR...H.NI..L....E... | |
| Retrocopy | YDIKALIGRGSFSRVVRVEHRATRQPYAIKMIETKYREGREVC-ESELRVLRRVRHANIIQLVEVFETQE |
| Parental | HLYLVMQLVSGGELFDRIVEKGFYTEKDASTLIRQVLDAVYYLHRMGIVHRDLKPENLLYYSQDEESKIM |
| ..Y.VM.L..GGELFDRI..KG..TE.DA......VLD.V.YLH..GI.HRDLKPENLLYY.....SKI. | |
| Retrocopy | RVYMVMELATGGELFDRIIAKGSFTERDATRVLQMVLDGVRYLHALGITHRDLKPENLLYYHPGTDSKII |
| Parental | ISDFGLSKMEGKGD--VMSTACGTPGYVAPEVLAQKPYSKAVDCWSIGVIAYILLCGYPPFYDENDSKLF |
| I.DFGL.....KGD...M.T.CGTP.Y.APEVL..KPY...VD.W..GVIAYILL.G..PF.D.N...L. | |
| Retrocopy | ITDFGLASARKKGDDCLMKTTCGTPEYIAPEVLVRKPYTNSVDMWALGVIAYILLSGTMPFEDDNRTRLY |
| Parental | EQILKAEYEF |
| .QIL...Y.. | |
| Retrocopy | RQILRGKYSY |
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 | 1 .08 RPM | 83 .62 RPM |
| SRP017611_kidney | 9 .28 RPM | 2 .16 RPM |
| SRP017611_liver | 2 .96 RPM | 14 .25 RPM |
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_1433 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_1433 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_rnor_1433 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 | ENSRNOG00000017882 | 1 retrocopy |
retro_rnor_1433 ,
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