RetrogeneDB ID: | retro_cfam_1761 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | 5:41108727..41109189(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | JAZF1 | ||
| Ensembl ID: | ENSCAFG00000003001 | ||
| Aliases: | None | ||
| Description: | JAZF zinc finger 1 [Source:HGNC Symbol;Acc:28917] |
Retrocopy-Parental alignment summary:
>retro_cfam_1761
GATACAGATCCAAGCGTTTTAGAACAAGAATTATAGCAGCCAACCTATGTTGCCCTCAGTTACGTGAATAGATTCATGAC
GGTTGCCACTTGCTGAGAGCCAGTCCCTAAAGAAGATTCACCTGAAGCTCTTGATGAGCTTGTCCAGCTCAGGGTCCTGA
AGGAATGTGTCCACTCCACCATGCCACAGCAGGGGAAGCCTTACTCCCCCCATTACTCTGCCCAACATCTCGTCCTCTTC
ATTCTGCAGCAACACCCCAACAGGCAGTGAGTACCACTGGGAGGAGGTGGATTATGAGGAATGGGACAGCGATGAGCCTG
GACCACAGAGAGTGCCATCAGCTCAGAAGCTATCCTCAGCTCCATGCACAAAAACGGAGAGGAAGAGAAGCCTTTTGTCT
GCCCGGTTCCTGGATGTAAAAAGAGATACAAGGTGAATGGTATAAAGTACCATGCTAAGGAC
ORF - retro_cfam_1761 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 70.62 % |
| Parental protein coverage: | 74.53 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | NTDPRVLEKQELQQPTYVALSYINRFMTDAA-RREQESLKKKIQPKLSLTLSSSVSRGNVSTPPRHSSGS |
| .TDP.VLE.QEL.QPTYVALSY.NRFMT.A.....Q...K.......SL...SS.S..NVSTPP.HS.GS | |
| Retrocopy | DTDPSVLE-QEL*QPTYVALSYVNRFMTVAT>AESQSLKKIHLKLLMSLS--SSGS*RNVSTPPCHSRGS |
| Parental | LTPPVTPPITPSSSFRSSTPTGSEYDEEEVDYEESDSDE-SWTTESAISSEAILSSMCMNGGEEKPFACP |
| LTPP.T.P...SSSF.S.TPTGSEY..EEVDYEE.DSDE..WTTESAISSEAILSSM..NG.EEKPF.CP | |
| Retrocopy | LTPPITLPNISSSSFCSNTPTGSEYHWEEVDYEEWDSDE<AWTTESAISSEAILSSMHKNGEEEKPFVCP |
| Parental | VPGCKKRYKNVNGIKYHAKN |
| VPGCKKRYK.VNGIKYHAK. | |
| Retrocopy | VPGCKKRYK-VNGIKYHAKD |
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 |
|---|---|---|
| SRP012049_cerebellum | 0 .04 RPM | 15 .79 RPM |
| SRP017611_brain | 0 .00 RPM | 14 .13 RPM |
| SRP017611_kidney | 0 .00 RPM | 2 .05 RPM |
| SRP017611_liver | 0 .00 RPM | 0 .44 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_1761 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_1761 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cfam_1761 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 | |
|---|---|---|---|
| Canis familiaris | ENSCAFG00000003001 | 1 retrocopy |
retro_cfam_1761 ,
|
| Felis catus | ENSFCAG00000023035 | 1 retrocopy | |
| Otolemur garnettii | ENSOGAG00000029759 | 1 retrocopy |