RetrogeneDB ID: | retro_rnor_2272 | ||
Retrocopy location | Organism: | Rat (Rattus norvegicus) | |
| Coordinates: | 6:6138497..6139258(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSRNOG00000004199 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Psme3 | ||
| Ensembl ID: | ENSRNOG00000036806 | ||
| Aliases: | Psme3, Ab2-371 | ||
| Description: | Glucose-6-phosphatase [Source:UniProtKB/Swiss-Prot;Acc:P43428] |
Retrocopy-Parental alignment summary:
>retro_rnor_2272
ATGGCCTCGTTGCTGAAGGTGGATCAGGAAGTTAAGCTCAAGGTTGATTCTTTCAGGGAGCGGATCACAAGTGAGGCAGA
AGACTTGGTGGCAAATTTTTTCCCAAAGAAGTTATTAGAACTTGATAGTTTTTTGAAGGAACCAATCCTAAATATCCATG
ACCTAACTCAAATCCACTCAGACATAAATCTCCCAGTCCCTGACCCCATTCTCCTCACCAATAGCCACGATGGACTGGAT
GGTCCCACTTACAAGAAGCGCAGGTTGGATGAATGTGAAGAGACCTTCCAAGGAACCAAGGTGTTTGTGATGCCCAACGG
GATGTTGAAAAGCAACCAGCAGCTTGTGGACGTTATTGACAAAGTAAAACCTGAGATTCGGCTGCTGATCGAGAAATGTA
ACATGGTCAAAATGTGGGCTCAGCTCTTGATTCCCAGGATAGAAGATGGGAACAACTTCCGGGTGTCGATTCAGGAGGAA
ACAGTTGCAGAGCTAAGAACTGTCGAGAGTGAAGCTGTATCTTATCTGGACCAGATTTCTAGATATTATATTACAAGAGC
CAAATTGGTTTCTAAATAGCTAAATACCCCCATGTGGAGGACTGTCGCCACACTGTCACAGAGATCGATGAGAAAGAGTA
CATCAGCCTCCGCCTCAGCATCTCAGAGCTGAGGAATCAGTATGTCACGCTCCATGACATGATCCTGAAAAACATTGAGA
AGATCAAACGGCCCCGAAGCAGCAATGAAGAGACACTGTAC
ORF - retro_rnor_2272 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 94.9 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MASLLKVDQEVKLKVDSFRERITSEAEDLVANFFPKKLLELDSFLKEPILNIHDLTQIHSDMNLPVPDPI |
| MASLLKVDQEVKLKVDSFRERITSEAEDLVANFFPKKLLELDSFLKEPILNIHDLTQIHSD.NLPVPDPI | |
| Retrocopy | MASLLKVDQEVKLKVDSFRERITSEAEDLVANFFPKKLLELDSFLKEPILNIHDLTQIHSDINLPVPDPI |
| Parental | LLTNSHDGLDGPTYKKRRLDECEEAFQGTKVFVMPNGMLKSNQQLVDIIEKVKPEIRLLIEKCNTVKMWV |
| LLTNSHDGLDGPTYKKRRLDECEE.FQGTKVFVMPNGMLKSNQQLVD.I.KVKPEIRLLIEKCN.VKMW. | |
| Retrocopy | LLTNSHDGLDGPTYKKRRLDECEETFQGTKVFVMPNGMLKSNQQLVDVIDKVKPEIRLLIEKCNMVKMWA |
| Parental | QLLIPRIEDGNNFGVSIQEETVAELRTVESEAASYLDQISRYYITRAKLVSK-IAKYPHVEDYRRTVTEI |
| QLLIPRIEDGNNF.VSIQEETVAELRTVESEA.SYLDQISRYYITRAKLVSK.IAKYPHVED.R.TVTEI | |
| Retrocopy | QLLIPRIEDGNNFRVSIQEETVAELRTVESEAVSYLDQISRYYITRAKLVSK<IAKYPHVEDCRHTVTEI |
| Parental | DEKEYISLRLIISELRNQYVTLHDMILKNIEKIKRPRSSNAETLY |
| DEKEYISLRL.ISELRNQYVTLHDMILKNIEKIKRPRSSN.ETLY | |
| Retrocopy | DEKEYISLRLSISELRNQYVTLHDMILKNIEKIKRPRSSNEETLY |
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 | 78 .37 RPM |
| SRP017611_kidney | 0 .00 RPM | 484 .85 RPM |
| SRP017611_liver | 0 .07 RPM | 427 .90 RPM |
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_2272 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_2272 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_rnor_2272 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Rattus norvegicus | ENSRNOG00000036806 | 3 retrocopies |
retro_rnor_2272 , retro_rnor_447, retro_rnor_448,
|