RetrogeneDB ID: | retro_cfam_1666 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | 4:63044279..63045380(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | EXOG | ||
| Ensembl ID: | ENSCAFG00000005039 | ||
| Aliases: | EXOG, ENDOGL1 | ||
| Description: | endo/exonuclease (5'-3'), endonuclease G-like [Source:HGNC Symbol;Acc:3347] |
Retrocopy-Parental alignment summary:
>retro_cfam_1666
GTTGCTGCTCAAGCTTTTGCTCCCCGCCTCCGAGGCTGCGGGCGCTCTCTGGGCATCTTGGTGGCCGGAGCTGCGGTGGG
TGCCGCGGGTGGCGAGTTCAGGGCCGGGCAGTTGCTCCAGAGGCAGGGCGTGGAGGCGGCGCTGGCAGTGAGGGAGCCCC
ACGGTTCTGCAGAGAAGTCTCTCTTAGAACAATCTGGAGTCCCTTTAACTGGAACAGAATCTAGGCTTTACACTAATCCT
GCCTTGCCTTATGATCAGTCAAAGCGGGTGGCCAGATGGGTTCTCCAACATACATCCAAGAGCAAGATAATGAGTGATGC
CAACAGAACATACTGTAAATTCAAGCCTGATCCCAACATCCTGCCAACCTTCAGTGCCTTCAATGAAGACTATCTTGGGA
GTGGGTAGTCAGGAGGACACATGGCTCCAGCAGGAAATGACAAATTTTCATCTAAAGCCATGGCTGAAACTTTTTGCTTT
TCTAATATTGTGCCTCAGAATTTTGATAATAATGCTGGGTATTGGAACAGAATAGAAATGTACCGTCGAGAACTGACAGA
GAGGTTTGAAGATGTCTGGATAGTACTTGGACCATTGACCTTTCCTCAGACTGGAAATGATGGAGAGAAAACCATTAGTT
ACGAGGGGATTGGTGAGGACAATGTGGCAGTCCCCTCACACCTTTATAAAGTGATCCTGCTCACAGAAGCCCGACTCTGC
TGAACCCCTGGCACGAGGGGCCTTCGTGGTGCCCAGTGAAGCCATTGGCCTCCAACCTCGGTTAAGTGAATTCCAAGCGA
GCCTTCAGGACCTGGAGAAGTTGTCAGGACTGGTGTTTTTTCCTCATTTGGATAGAACTGGTGGTATCAGGAATATCTGC
TCTGTGGACACCTGTAAGCTCCTGGATTTCCAGGAGTCCACTCTGTACCTGAGCACAAGAAAGACTGAGGGAACCCGATC
AGTACTCAGGCTGGAAAAGATCATGGAACATTTGAAGAATGCAGGGATTGAACCGATGATTCCTTCATGAGCCGCTATAA
GAAGAAGCTAGAAGAACTCCAAGCTAAGGCGCAGGCAGGATTCCTGGAGAGAAAAACATCT
ORF - retro_cfam_1666 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 83.56 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | MAAKSFASRLGGSGRSLGVFVAGAAVGAAGGGFAAVQWLERQSAEAAPAVREPDGSAEKSLLEQFGVPLT |
| .AA..FA.RL.G.GRSLG..VAGAAVGAAGG.F.A.Q.L.RQ..EAA.AVREP.GSAEKSLLEQ.GVPLT | |
| Retrocopy | VAAQAFAPRLRGCGRSLGILVAGAAVGAAGGEFRAGQLLQRQGVEAALAVREPHGSAEKSLLEQSGVPLT |
| Parental | GTETRHYTNHALSYDQSKRVPRWVLEHISKSKIMGDANRKHCKFKPDPNIPPTFSAFNEDYIGSGWSRGH |
| GTE.R.YTN.AL.YDQSKRV.RWVL.H.SKSKIM.DANR..CKFKPDPNI.PTFSAFNEDY.GSG.S.GH | |
| Retrocopy | GTESRLYTNPALPYDQSKRVARWVLQHTSKSKIMSDANRTYCKFKPDPNILPTFSAFNEDYLGSG*SGGH |
| Parental | MAPAGNNKFSSKAMAETFYLSNIVPQNFDNNAGYWNRIEMYCRELTERFEDVWIVSGPLTLPQTGSDGKK |
| MAPAGN.KFSSKAMAETF..SNIVPQNFDNNAGYWNRIEMY.RELTERFEDVWIV.GPLT.PQTG.DG.K | |
| Retrocopy | MAPAGNDKFSSKAMAETFCFSNIVPQNFDNNAGYWNRIEMYRRELTERFEDVWIVLGPLTFPQTGNDGEK |
| Parental | TVSYQVIGEDNVAVPSHLYKVIL-ARRSPT-SAEPLALGAFVVPNEAIGFQPQLNEFQVSLQDLEKLSGL |
| T.SY..IGEDNVAVPSHLYKVIL.A.RSPT.SAEPLA.GAFVVP.EAIG.QP.L.EFQ.SLQDLEKLSGL | |
| Retrocopy | TISYEGIGEDNVAVPSHLYKVIL<AHRSPT<SAEPLARGAFVVPSEAIGLQPRLSEFQASLQDLEKLSGL |
| Parental | VFFPHLDRTSGIRNICSVDTCKLLDFQEFTLYLSTRKIEGARSVLRLEKIMEHLKNAGIEP-DDSFMSRY |
| VFFPHLDRT.GIRNICSVDTCKLLDFQE.TLYLSTRK.EG.RSVLRLEKIMEHLKNAGIEP.DDSFMSRY | |
| Retrocopy | VFFPHLDRTGGIRNICSVDTCKLLDFQESTLYLSTRKTEGTRSVLRLEKIMEHLKNAGIEP<DDSFMSRY |
| Parental | KKKLEELQAKEQAGILERNSS |
| KKKLEELQAK.QAG.LER..S | |
| Retrocopy | KKKLEELQAKAQAGFLERKTS |
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 .00 RPM | 10 .42 RPM |
| SRP017611_brain | 0 .00 RPM | 10 .16 RPM |
| SRP017611_kidney | 0 .00 RPM | 11 .36 RPM |
| SRP017611_liver | 0 .00 RPM | 7 .25 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_1666 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_1666 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cfam_1666 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 | ENSCAFG00000005039 | 1 retrocopy |
retro_cfam_1666 ,
|
| Sorex araneus | ENSSARG00000009026 | 1 retrocopy | |
| Tupaia belangeri | ENSTBEG00000011185 | 1 retrocopy |