RetrogeneDB ID: | retro_cfam_2134 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | X:12287948..12289247(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCAFG00000012233 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ENO3 | ||
| Ensembl ID: | ENSCAFG00000015802 | ||
| Aliases: | None | ||
| Description: | enolase 3 (beta, muscle) [Source:HGNC Symbol;Acc:3354] |
Retrocopy-Parental alignment summary:
>retro_cfam_2134
ATGTCTATTCTCAAGATCCACGCCAGGGAGATCTTTGACTCTCGTGGGAACCCCACTGTTGAGGTTGACCTCTACACCTC
CAAAGGTCTCTTCAGAGCTGCTGTGCCCAGTGGTGCCTCCACTGGTATCTACGAGGCCCTCGAGCTCCGGGACAATGACA
AGACACGCTACATGGGGAAAGGTGTCTCAAAGGCTGTTGAGCACATCAATAAAACTATTGCACCTGCCCTGGTTAGCAAG
AAAGTGAACGTTGTGGAGCAGGAAAAGATTGACAAACTGATGATCAAGATGGACGGGACAGAGAATAAATCTAAATTTGG
TGCAAATGCCATTCTGGAGTGTCCCTGGCTGTCTGCAAGGCGGGGGCTGTCGAGAAGGGGGTGCCCCTGTACCGCCACAT
TGCTGATTTGGCTGGCAATTCTGAAGTTATCCTGCCAGTTCCGGCTTTCAATGTCATCAAGGTGGTTCCCATGCTGGCAA
CAAGCTGGCCATGCAGGAGTTCATGATCCTTCCCGTTGGTGCAGCGAACTTCAAGGAGGCCATGCGCATCGGAGCAGAGG
TTTATCACAACCTGAAGAATGTCATCAAGGAGAAATATGGAAAAGATGCCACCAATGTGGGCGATGAAGGTGGATTTGCT
CCTAATATCCTGGAGAACAAAGAAGCTCTGGAACTGCTGAAGAATGCCATCGGGAAGGCTGGCTACACCGATAAGGTGGT
CATCGGCATGGACATAGCTGCTTCCGAGTTCTTCAGGTCTGGAAGTATGACCTGGACTTCAAGTCCCCTGATGACCCCAG
CAGGTACATCACGCCTGACCAGCTGGCTGACCTCTACAAGTCCTTCATCAGGAACTACCCAGTGGCGTCTTTTGAAGACC
CCTTCAACCAGGATGACTGGGAAGTTTGGCAGAACTTCACTGCCAGCGCTGGAATCCAAGTGGTGGGGGACGATCTCACC
GTGACCAACCCGAAGCAGATTTCCAAGGCTGTGGGCAAGAAATCGTGCAACTGCCTCCTGCTTAAAGTGAACCAGATTGG
CTCTGTGACCGAGTCTCTTCAGGCGTGCAAGCTGGCCCAGTCCAATGGGTGGGGCGTCATGGTGTCGCATCGCTCTGGGG
AGACCAAAGATACCTTTATCGCTGACCTGGTGGTGGGACTCTGCACTGGGCAGGTCAAGACAGGTGCACCATGCAGATCC
GAGCGCTTGGCCAAGTACAACCAGATCCTCAGAATTGAAGAGGAACTGGGTAGCAAGGCCAAGTTCGTCGGCAGAAGCTT
CAGAAACCCCCTTGCCAAG
ORF - retro_cfam_2134 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 81.01 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | MAMQKIFAREILDSRGNPTVEVDLHTAKGRFRAAVPSGASTGIYEALELRDGDKSRYLGKGVLKAVEHIN |
| M...KI.AREI.DSRGNPTVEVDL.T.KG.FRAAVPSGASTGIYEALELRD.DK.RY.GKGV.KAVEHIN | |
| Retrocopy | MSILKIHAREIFDSRGNPTVEVDLYTSKGLFRAAVPSGASTGIYEALELRDNDKTRYMGKGVSKAVEHIN |
| Parental | KTLGPALLEKKLSVVDQEKVDKFMIELDGTENKSKFGANAIL-GVSLAVCKAGAAEKGVPLYRHIADLAG |
| KT..PAL..KK..VV.QEK.DK.MI..DGTENKSKFGANAIL.GVSLAVCKAGA.EKGVPLYRHIADLAG | |
| Retrocopy | KTIAPALVSKKVNVVEQEKIDKLMIKMDGTENKSKFGANAIL<GVSLAVCKAGAVEKGVPLYRHIADLAG |
| Parental | NPDLVLPVPAFNVIN-GGSHAGNKLAMQEFMILPVGASSFREAMRIGAEVYHHLKGVIKAKYGKDATNVG |
| N....LPVPAFNVI..GGSHAGNKLAMQEFMILPVGA..F.EAMRIGAEVYH.LK.VIK.KYGKDATNVG | |
| Retrocopy | NSEVILPVPAFNVIK<GGSHAGNKLAMQEFMILPVGAANFKEAMRIGAEVYHNLKNVIKEKYGKDATNVG |
| Parental | DEGGFAPNILENNEALELLKTAIQAAGYPDKVVIGMDVAASEFYRNG-KYDLDFKSPDDPARHITGEKLG |
| DEGGFAPNILEN.EALELLK.AI..AGY.DKVVIGMD.AASEF.R.G.KYDLDFKSPDDP.R.IT...L. | |
| Retrocopy | DEGGFAPNILENKEALELLKNAIGKAGYTDKVVIGMDIAASEFFRSG<KYDLDFKSPDDPSRYITPDQLA |
| Parental | ELYKSFIKNYPVVSIEDPFDQDDWATWTSFLSGVNIQIVGDDLTVTNPKRIAQAVEKKACNCLLLKVNQI |
| .LYKSFI.NYPV.S.EDPF.QDDW..W..F.....IQ.VGDDLTVTNPK.I..AV.KK.CNCLLLKVNQI | |
| Retrocopy | DLYKSFIRNYPVASFEDPFNQDDWEVWQNFTASAGIQVVGDDLTVTNPKQISKAVGKKSCNCLLLKVNQI |
| Parental | GSVTESIQACKLAQSNGWGVMVSHRSGETEDTFIADLVVGLCTGQIKTGAPCRSERLAKYNQLMRIEEAL |
| GSVTES.QACKLAQSNGWGVMVSHRSGET.DTFIADLVVGLCTGQ.KTGAPCRSERLAKYNQ..RIEE.L | |
| Retrocopy | GSVTESLQACKLAQSNGWGVMVSHRSGETKDTFIADLVVGLCTGQVKTGAPCRSERLAKYNQILRIEEEL |
| Parental | GDKAVFAGRKFRNPKAK |
| G.KA.F.GR.FRNP.AK | |
| Retrocopy | GSKAKFVGRSFRNPLAK |
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 | 32 .26 RPM | 15 .88 RPM |
| SRP017611_brain | 34 .14 RPM | 6 .51 RPM |
| SRP017611_kidney | 49 .20 RPM | 3 .30 RPM |
| SRP017611_liver | 18 .56 RPM | 20 .38 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_2134 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_2134 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cfam_2134 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 4 parental genes, and 30 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Canis familiaris | ENSCAFG00000014523 | 1 retrocopy | |
| Canis familiaris | ENSCAFG00000015802 | 2 retrocopies |
retro_cfam_1010, retro_cfam_2134 ,
|
| Callithrix jacchus | ENSCJAG00000011679 | 2 retrocopies | |
| Macropus eugenii | ENSMEUG00000007915 | 25 retrocopies |
retro_meug_1019, retro_meug_1341, retro_meug_1483, retro_meug_1540, retro_meug_1566, retro_meug_1605, retro_meug_170, retro_meug_1701, retro_meug_1743, retro_meug_1869, retro_meug_1905, retro_meug_1929, retro_meug_2026, retro_meug_2190, retro_meug_235, retro_meug_269, retro_meug_578, retro_meug_607, retro_meug_637, retro_meug_803, retro_meug_820, retro_meug_906, retro_meug_965, retro_meug_973, retro_meug_976,
|