RetrogeneDB ID: | retro_fcat_470 | ||
Retrocopy location | Organism: | Cat (Felis catus) | |
| Coordinates: | A3:57009662..57010462(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | LRRC17 | ||
| Ensembl ID: | ENSFCAG00000009938 | ||
| Aliases: | None | ||
| Description: | leucine rich repeat containing 17 [Source:HGNC Symbol;Acc:16895] |
Retrocopy-Parental alignment summary:
>retro_fcat_470
GACAACCCGTGGCATGTACTCATGAGATGGAAATGCTTATTTCAATGTTGCGGATTCCAAGAAACCCGGATTTGGGGAAC
TACACCAAGTGTGAAAGCCCACAAGATCTAAAAATCAAAAACTGCTGCAGATAAACCTTGAACAGTTATGAAATGAAGAA
GAAAGGGAACAATTAGACCTGAAACCCCAATGTCAGGGAGACCCCCAGTCATCAAGCCTGAGGTAGACTCTTCTCTTTGC
TCCAATTACATGTTTCCCATACAAACGTTGGACTGCAAACAGAAAGAGTAGAAGAAAGTTCCAAACAACATCCCTCCAGA
CATTGTTAAACTTGACTTGTCATACAATGAAATCAACCAGCTTTGATCCAAGGAGTTTGAAGATATTCGTGAGCTAAAAA
AATTAAACCTCAGCAGCAATGGTATTGAATTCATAGATACTGGTGCTTTTTTAGGATTCACACATTTAGAAGAGTTAGAA
TTATCAAACAAAAGTCTACAAAACTATGATTGTGGTGTATTAGAAGACTTGTATTTTTTGCAACTCTTGTGGATCAGAGA
TACCCTTGGAAATGTGACTACAATATCCACTACCTCTACTACTGGTTAAAGCACCACTACAACGTACAATATAATGGCCT
GGGATGCAAGATGGCTGAAGAATACACAGGGTGGTTTGTGGGAAAATATGTTCACAGTTACTTTGAAGAATGCCCCAAAG
ACAAATTACACCCTGAGACATTTGATCAAGGTCAAGAAGATGATGACTGGGAGAAGATTCATAGGGATCATGTAGCAGAG
ORF - retro_fcat_470 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 81.02 % |
| Parental protein coverage: | 61.22 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | DNPWH-CTCEMETLISMLQIPRNRNLGNYAKCERPQDLK-NKKLRQIKSEQLCNEEEREQLDPKPQ-VSG |
| DNPWH.CT.EME.LISML.IPRN..LGNY.KCE.PQDLK.N.KL.QI..EQL.NEEEREQLD.KPQ..SG | |
| Retrocopy | DNPWH<CTHEMEMLISMLRIPRNPDLGNYTKCESPQDLK<NQKLLQINLEQL*NEEEREQLDLKPQ<MSG |
| Parental | RPPVIKPEVDSTLCYNYVFPIQTLDCKRKELKKVPNNIPPDIVKLDLSYNKINQLRPKEFEDVHELKKLN |
| RPPVIKPEVDS.LC.NY.FPIQTLDCK.KE.KKVPNNIPPDIVKLDLSYN.INQL..KEFED..ELKKLN | |
| Retrocopy | RPPVIKPEVDSSLCSNYMFPIQTLDCKQKE*KKVPNNIPPDIVKLDLSYNEINQL*SKEFEDIRELKKLN |
| Parental | LSSNGIEFIDPAAFLGLTHLEELDLSNNSLQNFDYGVLEDLYFLKLLWLRDN-PWRCDYNIHYLYYWLKH |
| LSSNGIEFID..AFLG.THLEEL.LSN.SLQN.D.GVLEDLYFL.LLW.RD..PW.CDYNIHYLYYWLKH | |
| Retrocopy | LSSNGIEFIDTGAFLGFTHLEELELSNKSLQNYDCGVLEDLYFLQLLWIRDT<PWKCDYNIHYLYYWLKH |
| Parental | HYNVHYNGLECKMPEEYKGWFVGKYVRSYFEECPKDKLPAYPETFDQDPEDDEWEKIHRDHTAK |
| HYNV.YNGL.CKM.EEY.GWFVGKYV.SYFEECPKDKL...PETFDQ..EDD.WEKIHRDH.A. | |
| Retrocopy | HYNVQYNGLGCKMAEEYTGWFVGKYVHSYFEECPKDKL--HPETFDQGQEDDDWEKIHRDHVAE |
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 | 0 .80 RPM |
| SRP017611_kidney | 0 .00 RPM | 1 .44 RPM |
| SRP017611_liver | 0 .00 RPM | 0 .30 RPM |
Felis catus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_fcat_470 retrocopy.
Felis catus was not studied using FANTOM5 data.
retro_fcat_470 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 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Choloepus hoffmanni | ENSCHOG00000013916 | 1 retrocopy | |
| Felis catus | ENSFCAG00000009938 | 1 retrocopy |
retro_fcat_470 ,
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