RetrogeneDB ID: | retro_fcat_1122 | ||
Retrocopy location | Organism: | Cat (Felis catus) | |
| Coordinates: | C1:129736821..129737223(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RAB40C | ||
| Ensembl ID: | ENSFCAG00000030517 | ||
| Aliases: | None | ||
| Description: | RAB40C, member RAS oncogene family [Source:HGNC Symbol;Acc:18285] |
Retrocopy-Parental alignment summary:
>retro_fcat_1122
ATCGACTACAAGACAACTACCAACCTGCCGGGCGGCCAGCGGGTCAAGCTGGAGTTCTCCAATACGTTGGGCGGAGGCAG
GTTCTGCACGGTGTTCAGGTCTTACTCCAGGGGCTCGCAGAGGATCCTCCTAGTGTGTGACATCACCAACAGCTGGTCCT
TGGACAGCTCGGATGGGCGTATCAAGGGGATCAAGGAGCCAGCCCGCCGGGGTCTCCTGGATCCTGGCAGGGAATGGAGC
CTCCAGGTAGCAAGTCGCCAAGGAGCAGGAGCGCACCTGCAGGGAGAACGGCCCAACCTTTTTCAAGTTAGGTCAGCTGT
GCAACTTCAGCTTCTTCAGGTCCTCAGCTGAGCTGTCCCACGTCGTGCTCATGCAGCATGGCGTGAAGATCTGTTCAGGC
CA
ORF - retro_fcat_1122 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 57.14 % |
| Parental protein coverage: | 56.33 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | IDYKTTTILLDGRRVKLELWDTSGQGRFCTIFRSYSRGAQGILLVYDITNRWSFDGIDRWIKEIDEHA-P |
| IDYKTTT.L..G.RVKLE...T.G.GRFCT.FRSYSRG.Q.ILLV.DITN.WS.D..D..IK.I.E.A.. | |
| Retrocopy | IDYKTTTNLPGGQRVKLEFSNTLGGGRFCTVFRSYSRGSQRILLVCDITNSWSLDSSDGRIKGIKEPA>A |
| Parental | GVPRILVGNRLHLAFKRQVPTEQARAYAEKNGMTFFEVSPLCNFNVIESFTELSRIVLMRHGM-EKIWRP |
| GV..IL.GN....A...QV..EQ.R...E.NG.TFF....LCNF....S..ELS..VLM.HG..E...RP | |
| Retrocopy | GVSWILAGNG---ASR*QVAKEQERTCRE-NGPTFFKLGQLCNFSFFRSSAELSHVVLMQHGV<EDLFRP |
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 | 13 .20 RPM |
| SRP017611_kidney | 0 .00 RPM | 34 .73 RPM |
| SRP017611_liver | 0 .00 RPM | 9 .20 RPM |
Felis catus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_fcat_1122 retrocopy.
Felis catus was not studied using FANTOM5 data.
retro_fcat_1122 was not experimentally validated.
Retrocopy orthology:
Felis catus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Felis catus | ENSFCAG00000030517 | 1 retrocopy |
retro_fcat_1122 ,
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