RetrogeneDB ID: | retro_cfam_1010 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | 21:18766478..18767556(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCAFG00000030498 | |
| 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_1010
CTAAACCTAACTCTTGCACCTGCCCTGACTAGCAAGAAGTGAACGTTGTGGAGCAGGAAAAGATTGACAAACTGATGATC
GAGATGGACGGGACAGAGAATAAATCTAAATTTGGTGCAAACGCTATTCTGGGAGTGTCCCTGGCTGTCTGCAAGGCAGG
GGCTGTCGAGAAGGAGGTGCCCCCGTACCACCACATTGCTGACTTGGCTGGCAATTCTGAAGTTATCCTGCCAGTTCCGG
CTTTCAATGTCATCAACGGTGGTTCCCATGCTGGCAACAAGCTGGCCGTGCAGGAGTTCATGATCCTTCTCATTGGTACA
GCTAACTTCAAGGAGGACATGCACATGGGGGAGACGATTTATCACAACCTGAAGAATGTCATCAAGAAGAAATAGGGAAA
AGATGCCACCAATGTGGGCGATGAAGGTGGATTTGCTCCTAATATCCTGGAGAACAAAGAAGCTCTGGAACTGCTGAAGA
ATGCCATCGGGAAGGCTGGCTACACCGATAAGGTGGTCACCGCATGGATGTAGCTGCTTCCGAGTTCTTCAGGTCTGGGA
AGTATGACCTGGACTTCAAGTCCCCTGATGACCCCAGAAGGTACATCACTCCTGACCGGCTGGCTGACCTCTACAAGTCC
TTCATCAGGGGCTACCCACTGGTGTCTATCGAAGACCCCTTTGACCAGGATGTCTGGGAAGCTTGGCAGAAGTTCACTGG
AATCCAGGTGGTAGGGGACGATCTCACCGTGACCAACCTGAAGCGGATTTCTGAGGCTGTGGGCGAGAAATCATGCAACT
GCCTCCTGCTTAAAGTGAACCAGATTGGCTCTGTGACCGAGTCTCTTGAGGTGTGCAAGCTGACCCAGTCCAATGGGTGG
GGCGTCATGGTGTCGCATTGCTCCGGGGAGATCGAAGATACCTTCATCGCCGACCTGGTGGTGGGACTCTGCACTGGGCA
GATCAAGACGGGTACACCATGCAGATCCGAGCACTTGGCCAAAGACAACCAGATCCTCAGAACTGAAGAGGAACTGGGTA
GCAAGGCCAAGTTCGCCGGCAGAAGCTTCAGAAACCCC
ORF - retro_cfam_1010 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 75.34 % |
| Parental protein coverage: | 83.64 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | INKTLGPALLEKK-LSVVDQEKVDKFMIELDGTENKSKFGANAILGVSLAVCKAGAAEKGVPLYRHIADL |
| .N.TL.PAL..KK...VV.QEK.DK.MIE.DGTENKSKFGANAILGVSLAVCKAGA.EK.VP.Y.HIADL | |
| Retrocopy | LNLTLAPALTSKK<VNVVEQEKIDKLMIEMDGTENKSKFGANAILGVSLAVCKAGAVEKEVPPYHHIADL |
| Parental | AGNPDLVLPVPAFNVINGGSHAGNKLAMQEFMILPVGASSFREAMRIGAEVYHHLKGVIKAKYGKDATNV |
| AGN....LPVPAFNVINGGSHAGNKLA.QEFMIL..G...F.E.M..G...YH.LK.VIK.K.GKDATNV | |
| Retrocopy | AGNSEVILPVPAFNVINGGSHAGNKLAVQEFMILLIGTANFKEDMHMGETIYHNLKNVIKKK*GKDATNV |
| Parental | GDEGGFAPNILENNEALELLKTAIQAAGYPDKVVIG-MDVAASEFYRNGKYDLDFKSPDDPARHITGEKL |
| GDEGGFAPNILEN.EALELLK.AI..AGY.DKVV...MDVAASEF.R.GKYDLDFKSPDDP.R.IT...L | |
| Retrocopy | GDEGGFAPNILENKEALELLKNAIGKAGYTDKVVTA<MDVAASEFFRSGKYDLDFKSPDDPRRYITPDRL |
| Parental | GELYKSFIKNYPVVSIEDPFDQDDWATWTSFLSGVNIQIVGDDLTVTNPKRIAQAVEKKACNCLLLKVNQ |
| ..LYKSFI..YP.VSIEDPFDQD.W..W..F.....IQ.VGDDLTVTN.KRI..AV..K.CNCLLLKVNQ | |
| Retrocopy | ADLYKSFIRGYPLVSIEDPFDQDVWEAWQKF---TGIQVVGDDLTVTNLKRISEAVGEKSCNCLLLKVNQ |
| Parental | IGSVTESIQACKLAQSNGWGVMVSHRSGETEDTFIADLVVGLCTGQIKTGAPCRSERLAKYNQLMRIEEA |
| IGSVTES...CKL.QSNGWGVMVSH.SGE.EDTFIADLVVGLCTGQIKTG.PCRSE.LAK.NQ..R.EE. | |
| Retrocopy | IGSVTESLEVCKLTQSNGWGVMVSHCSGEIEDTFIADLVVGLCTGQIKTGTPCRSEHLAKDNQILRTEEE |
| Parental | LGDKAVFAGRKFRNP |
| LG.KA.FAGR.FRNP | |
| Retrocopy | LGSKAKFAGRSFRNP |
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 | 15 .88 RPM |
| SRP017611_brain | 1 .51 RPM | 6 .51 RPM |
| SRP017611_kidney | 2 .31 RPM | 3 .30 RPM |
| SRP017611_liver | 0 .65 RPM | 20 .38 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_1010 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_1010 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cfam_1010 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,
|