RetrogeneDB ID: | retro_cfam_1428 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | 31:13127..14071(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RAP1GDS1 | ||
| Ensembl ID: | ENSCAFG00000010267 | ||
| Aliases: | None | ||
| Description: | RAP1, GTP-GDP dissociation stimulator 1 [Source:HGNC Symbol;Acc:9859] |
Retrocopy-Parental alignment summary:
>retro_cfam_1428
GCAGATACTCTCAGTGATACCTTGAAGAAGTTGAAGATAACAGCTGTTGACAGAACTGAAGATAGTTTAGAAGGATGCTT
GGATTGTCTGCTTCAAGCCCTGGCTCAAAATAATATGGAAACGAGTGAAAAAAATCCAAGGAAGTGGAATACTTCAGCTG
TTTGTAAGTCTGTTGATTCCACAGTCTTCCTGCACAGCCAAAGTAGCTAACGTCATAGCAGAAGTAGCCAAAAATGAATG
TATGTGTATTCCATGTATGGATACTGGATTGACTTCACCATTGGTGCAGCTGCTAAATAGCAAAGACCAGGAAGTGCTAC
TTCAAATGGGCAGGGCTCTGGGAAGCATATGTTACGATAGCCATGAGGGCAGAAGTGCAGTTGATCAAGCAGGTGGTGCA
CAGATTGTAATTGACCATTTAAGGTCACTGTGCAGTATAACAGATCCCACCAATGAAAAGCTCTTGACTGTCTTTTGTGG
TATGCTGATGAACTACAGCAATGAGAATGATTCCCTTCAAGCTCAGCTTATCAATATGGGTGTTATACCTACCCCAGTGA
AATTACTGGGCATCCATTGCCAAAATGCAGCTCGTACAGAAATGTGTCTTGTTGCATTTGGTAACTTAGCAGAACTTGAG
TCAAGTAAAGAACAGTTTGCCAGTACGAACATTGCTGAAGAGCTAGTAAAACTCTTTAAGAAACAAATAGAACATGATAA
AAGGGAAATGATTTTGGAAGTTCTTGCTCCACTGGCAGAAAAATGATGCTATTAAACTACAGCTGGTTGAAGCAGGCCTG
GTAGAGTGTCTACTAGAGATTGTTCAGCAGAAAGTGGATAGTGACAAAGGGCATGATATTGCTGAGCTCAAAACCGCTTC
AGATCTAATGGTTTTTCTACTTCTTGGAGATGAATCCATGCAGAAATTATTTGAAGTAGGAAAA
ORF - retro_cfam_1428 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 91.46 % |
| Parental protein coverage: | 51.73 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | ADNLSDTLKKLKITAVDRTEDSLEGCLDCLLQ-PWLKIDMETSEKIQGSGILQLFASLLIPQSSCTAKVA |
| AD.LSDTLKKLKITAVDRTEDSLEGCLDCLLQ.PWLKI......KIQGSGILQLF.SLLIPQSSCTAKVA | |
| Retrocopy | ADTLSDTLKKLKITAVDRTEDSLEGCLDCLLQ>PWLKIIWKRVKKIQGSGILQLFVSLLIPQSSCTAKVA |
| Parental | NIIAEVAKNEFMRIPCVDAGLISPLVQLLNSKDQEVLLQTGRALGNICYDSHEGRSAVDQAGGAQIVVDH |
| N.IAEVAKNE.M.IPC.D.GL.SPLVQLLNSKDQEVLLQ.GRALG.ICYDSHEGRSAVDQAGGAQIV.DH | |
| Retrocopy | NVIAEVAKNECMCIPCMDTGLTSPLVQLLNSKDQEVLLQMGRALGSICYDSHEGRSAVDQAGGAQIVIDH |
| Parental | LRSLCSITDPANEKLLTVFCGMLMNYSNENDSLQAQLINMGVIPTLVKLLGIHCQNAALTEMCLVAFGNL |
| LRSLCSITDP.NEKLLTVFCGMLMNYSNENDSLQAQLINMGVIPT.VKLLGIHCQNAA.TEMCLVAFGNL | |
| Retrocopy | LRSLCSITDPTNEKLLTVFCGMLMNYSNENDSLQAQLINMGVIPTPVKLLGIHCQNAARTEMCLVAFGNL |
| Parental | AELESSKEQFASTNIAEELVKLFKKQIEHDKREMIFEVLAPLAE-NDAIKLQLVEAGLVECLLEIVQQKV |
| AELESSKEQFASTNIAEELVKLFKKQIEHDKREMI.EVLAPLAE.NDAIKLQLVEAGLVECLLEIVQQKV | |
| Retrocopy | AELESSKEQFASTNIAEELVKLFKKQIEHDKREMILEVLAPLAE>NDAIKLQLVEAGLVECLLEIVQQKV |
| Parental | DSDKEDDIAELKTASDLMVLLLLGDESMQKLFEGGK |
| DSDK..DIAELKTASDLMV.LLLGDESMQKLFE.GK | |
| Retrocopy | DSDKGHDIAELKTASDLMVFLLLGDESMQKLFEVGK |
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 | 1 .09 RPM | 56 .36 RPM |
| SRP017611_brain | 1 .91 RPM | 106 .78 RPM |
| SRP017611_kidney | 0 .07 RPM | 12 .08 RPM |
| SRP017611_liver | 0 .36 RPM | 8 .92 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_1428 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_1428 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cfam_1428 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Canis familiaris | ENSCAFG00000010267 | 2 retrocopies |
retro_cfam_1428 , retro_cfam_370,
|