RetrogeneDB ID: | retro_cfam_2181 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | X:72438452..72439064(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCAFG00000024749 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PDCD7 | ||
| Ensembl ID: | ENSCAFG00000032076 | ||
| Aliases: | None | ||
| Description: | programmed cell death 7 [Source:HGNC Symbol;Acc:8767] |
Retrocopy-Parental alignment summary:
>retro_cfam_2181
CTAGAGGCGGTGTTCGGAACCCCTCGCGGGCAAGCTACCCTGTGCCTCCGCGCGTGCCCGCCGGGCCCAGGCTGGGCGAA
GTGCGCCGGTGGCTGCGAGAGGCTCTGCTCCTGGCGTGGCAGGGGCGTGGCCTGAGCCAGGCCCTGCGTGAGGCCGAGGT
GGATGGTGCGGCCTGGGTACTGCTACATGCCCAGCCAGCACCGCTGCGCACTGAATTGGTCGAGAGACTGCAGCTGCTGA
CCCAGGCCGCCTATGTGGATGAGGCGCGGGGGAGGCTGGAGAGGGTCCAGCGCCGCCGACTGCAGCTTAGCGAGAGGGTG
CTAGAACACGAGGCCGAGGCCGAGGCCAAGTGGAAAGCTGAGTGCGAGCAGGAGATTGACCTCTGGAGGGTCAAGTGCGT
TGCAGGAGGTGGAGAAGAAGCAGGAGCAGGAACTTAAAGCTGCTGCTGAAGGTGTCTTACCTGAAGTGAGGAAAAAGCAA
GGAAATACCAAAAGGATGGTGGACATTCTTCAGACCTTGGAGAAATTGAGGAAACTCAGGAAAGAGGCAGCAGCAAGGAA
AGGCGTCTGTCCTTCAGCTTCAGGGACTAAGAAAACTCATTTAAAAACTCTC
ORF - retro_cfam_2181 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 74.41 % |
| Parental protein coverage: | 57.42 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | LEAVVVTPR-RAGCPVPPRAPAGPSLGEVRARLRGALRLVRRLRDLGQALREAEADGAAWVLLHAQAAPL |
| LEAV..TPR.RA..PVPPR.PAGP.LGEVR..LR.AL.L....R.L.QALREAE.DGAAWVLLHAQ.APL | |
| Retrocopy | LEAVFGTPR<RASYPVPPRVPAGPRLGEVRRWLREALLLAWQGRGLSQALREAEVDGAAWVLLHAQPAPL |
| Parental | RAELAERLQLLTQAAYVGEARRRLERVRRRRLRLRERARERDAEREAEAARAAEREQEIDLWRVKCV-QE |
| R.EL.ERLQLLTQAAYV.EAR.RLERV.RRRL.L.ER..E..A..EAEA...AE.EQEIDLWRVKCV.QE | |
| Retrocopy | RTELVERLQLLTQAAYVDEARGRLERVQRRRLQLSERVLEHEA--EAEAKWKAECEQEIDLWRVKCV>QE |
| Parental | VEEKKREQELKAAADGVLSEVRKKQADTKRMVDILRALEKLRKLRKEAAARKGVCPPASADETFEHHLQR |
| V.EKK.EQELKAAA.GVL.EVRKKQ..TKRMVDIL..LEKLRKLRKEAAARKGVCP.AS...T...HL.. | |
| Retrocopy | V-EKKQEQELKAAAEGVLPEVRKKQGNTKRMVDILQTLEKLRKLRKEAAARKGVCPSASG--TKKTHLKT |
| Parental | L |
| L | |
| Retrocopy | L |
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 | 13 .69 RPM |
| SRP017611_brain | 0 .00 RPM | 12 .94 RPM |
| SRP017611_kidney | 0 .00 RPM | 5 .68 RPM |
| SRP017611_liver | 0 .00 RPM | 4 .28 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_2181 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_2181 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cfam_2181 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 | ENSCAFG00000032076 | 1 retrocopy |
retro_cfam_2181 ,
|
| Choloepus hoffmanni | ENSCHOG00000007218 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000014340 | 1 retrocopy |