RetrogeneDB ID: | retro_rnor_1969 | ||
Retrocopy location | Organism: | Rat (Rattus norvegicus) | |
| Coordinates: | 4:56030417..56030734(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Timp1 | ||
| Ensembl ID: | ENSRNOG00000010208 | ||
| Aliases: | Timp1, TIMP-1, Timp | ||
| Description: | Metalloproteinase inhibitor 1 [Source:UniProtKB/Swiss-Prot;Acc:P30120] |
Retrocopy-Parental alignment summary:
>retro_rnor_1969
CGGTTCGCCTACATCCCAGCCATGGAGAGTCTCTGTTGATATGTCCACAAGTTCCAAAACTGCAGCGAGGAGTTTCTCAT
CGCCGGCCGCCTAAGGAACGGAAATTTGCGCCTCAGCGCCTGCAGCTTCCTGGTTCTCTGGCTTAATCAGCCCTGCTAAG
CAAAGGCCTTAAAGACCTACAGTGCTGACCTTGGGGCGTGCACAGTGTTTCCCTGTTCAACCATCCCTTGCAAACTGGAG
AGTGACACTCATTCTTGTGGACAGATCAGATCCTCATGCTCTCTGAGAAGGGCTACCGGAGCAGTCACTGCCTGCCT
ORF - retro_rnor_1969 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 74.77 % |
| Parental protein coverage: | 50.69 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | RFAYTPAMESLCGYVHKSQNRSEEFLIAGRLRNGNLHITACSFLVPWHNLSPAQQKAFVKTYSAGCGVCT |
| RFAY.PAMESLC.YVHK.QN.SEEFLIAGRLRNGNL...ACSFLV.W.N..P...KA..KTYSA..G.CT | |
| Retrocopy | RFAYIPAMESLC*YVHKFQNCSEEFLIAGRLRNGNLRLSACSFLVLWLN-QPC*AKA-LKTYSADLGACT |
| Parental | VFPCSAIPCKLESDSHC-LWTDQILMGSEKGYQSDHFACLP |
| VFPCS.IPCKLESD.H..LWTDQILM.SEKGY.S.H..CLP | |
| Retrocopy | VFPCSTIPCKLESDTHS<LWTDQILMLSEKGYRSSH--CLP |
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 | 1 .15 RPM |
| SRP017611_kidney | 0 .00 RPM | 1 .95 RPM |
| SRP017611_liver | 0 .00 RPM | 0 .74 RPM |
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_1969 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_1969 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_rnor_1969 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Procavia capensis | ENSPCAG00000014112 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000010208 | 1 retrocopy |
retro_rnor_1969 ,
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