RetrogeneDB ID: | retro_rnor_1385 | ||
Retrocopy location | Organism: | Rat (Rattus norvegicus) | |
| Coordinates: | 18:21262465..21263132(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Tsen34 | ||
| Ensembl ID: | ENSRNOG00000011468 | ||
| Aliases: | Tsen34, LENG5, SEN34 | ||
| Description: | tRNA-splicing endonuclease subunit Sen34 [Source:RefSeq peptide;Acc:NP_001006969] |
Retrocopy-Parental alignment summary:
>retro_rnor_1385
GAGCAAAGTTTTCAGGATCAGAGCTCTTTGGCAGCAGAGGCCCAGCAGACCCGGGGACAGGAACTTCTAGAGAAGATCTT
GGAAGGCCAGGCTGCTAAGAAGCAGAGGCTGGAACAGGATTCAGGGGCAGATGAAGAAGGCCAAGAAGCTGGTGGAAGTG
AAGCTACCCAAGGAAGTGAGACCAGTGATGATGATCAGGCTTCTGCAGAACAGGAAGTAGCAGATTTTTCATCCCTCCAA
CCAGGACCTTCAAATGGGGTGACTCCCTTACCAAGATCAGCCCTGCTTATCTAGCTGGCCACTGCCAGACCTCGGCCTGT
AAAACCTAAGCCTCTGGACTGGCATGTGCAGACCAAAGCCTGGCCCTGTGCTGGCCGTCCTGCTCATGAGCTTTGCTACC
GCATCTACAGAGACCTGTGGGAGAGAAGCTTCTTCCTCAGTGCAGCTGGGAAGTTTGGTGGTGACTTCCTGGTCTATCCT
GGTGATCTGCTGCGTTTCCATGCTCACTACATTGCACAATGCTGGTCTGCTGAGGACCCCATCCCACTTCAGGACCTGGT
CTCTGTAGGCTGCCTGGGAAACCAGTGTCAGAAAGACTCTGCTTCTCTGCTCCCCTCAGCCTCATGGGAAGGTGATTTAT
ACTTCCCTGCAGTGGGCCAGCCTGCAG
ORF - retro_rnor_1385 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 88.79 % |
| Parental protein coverage: | 71.15 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | EQSFQDQSTLAAEARETRRQELLEKIVEGQAAKKQKLEQDSGADEEGQEAGGSEATQGSETSDDGQASAE |
| EQSFQDQS.LAAEA..TR.QELLEKI.EGQAAKKQ.LEQDSGADEEGQEAGGSEATQGSETSDD.QASAE | |
| Retrocopy | EQSFQDQSSLAAEAQQTRGQELLEKILEGQAAKKQRLEQDSGADEEGQEAGGSEATQGSETSDDDQASAE |
| Parental | QEGADSSSPQPGPSNGVTPLPRSALLIQLATARPRPVKAKPLDWRVQSKDWPHAGRPAHELRYSIYRDLW |
| QE.AD.SS.QPGPSNGVTPLPRSALLI.LATARPRPVK.KPLDW.VQ.K.WP.AGRPAHEL.Y.IYRDLW | |
| Retrocopy | QEVADFSSLQPGPSNGVTPLPRSALLI*LATARPRPVKPKPLDWHVQTKAWPCAGRPAHELCYRIYRDLW |
| Parental | ERGFFLSAAGKFGGDFLVYPGDPLRFHAHYIAQCWSAEDPIPLQDLVSAGRLG-TSVRKTLLLCSPQPDG |
| ER.FFLSAAGKFGGDFLVYPGD.LRFHAHYIAQCWSAEDPIPLQDLVS.G.LG.TSVRKTLLLCSPQP.G | |
| Retrocopy | ERSFFLSAAGKFGGDFLVYPGDLLRFHAHYIAQCWSAEDPIPLQDLVSVGCLG>TSVRKTLLLCSPQPHG |
| Parental | KVVYTSLQWASLQ |
| KV.YTSLQWASLQ | |
| Retrocopy | KVIYTSLQWASLQ |
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 .07 RPM | 0 .00 RPM |
| SRP017611_kidney | 0 .00 RPM | 0 .00 RPM |
| SRP017611_liver | 0 .00 RPM | 0 .00 RPM |
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_1385 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_1385 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_rnor_1385 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 | |
|---|---|---|---|
| Microcebus murinus | ENSMICG00000002409 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000035585 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000011468 | 1 retrocopy |
retro_rnor_1385 ,
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