RetrogeneDB ID: | retro_cfam_1407 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | 30:24751611..24752597(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSCAFG00000002325 | ||
| Aliases: | None | ||
| Description: | Glyceraldehyde-3-phosphate dehydrogenase [Source:UniProtKB/TrEMBL;Acc:E2RNN4] |
Retrocopy-Parental alignment summary:
>retro_cfam_1407
ATGGTGAAGGTCGGAGTGAACGGATTTGGCCGTATTGGGCGCCTGGTCACCAGGGCTGCTTTTAATTCTGGCAAAATGGA
TATTGTCGCCATCAATGACCCCTTCATTGACCTCAACCTCATGGTATACATGTTCCAGTATGATTCTACCCATGGCAAAT
TCCACAGCACAGTCAAGGCTGAGAATGGGAAACTTGTCATCAATGGGAAGTCCATCTCTATCTTCCAGGAGCGAGATCCT
GCCAACATCAAATGGGGTAATGCTGGTGCTGAGTATGTTGTGGAGTCCACTGGGGTCTTCACCACCATGGAGAAGGCTGG
GGCTCACTTGAAGGGTGGGGCCAAGAGGGTCATCATCTCTGCTCCTTCTGCTGATGCCCCCATGTTTGTGATGGGCGTGA
ACCACAAGAAGTATGACAACTCCCTCAAGATTGTCACAATGCTTCCTGCACCATCAATTGCTTGGCTTCTCTGGCCAAAG
TCATCCATGACCACTTTGGCATCATGGAGGGCCTCATGATCACTGTCCATGCCATCACTGCCACCCAGAAGACCGTGGAC
GGCCCCTCTGGGAAGCTGTGGCATGATGGCTGAGGGGATGCCCAGAACATCATCCCTGCTTTCACTGGCACTGCTAAGGC
TATGGGCAAGGTCATCCTTGAAGCTCACTGTATGGCCTTCCGTGTCCCCACCCCCAACATGTCAGTTGTGGATCTGACCG
GCCGCCTGGAGAAAGCTGCCAAATATGACAACATCAAGAAGGTGGTGAAGCAGGCATCAGAGGGCCCCCTCAAGGGCATC
CTGGGCTACACTGAGGACCAGGTTGTCTCCTGCAACTTCAACAGTGACACTCACTCTTCCACCTTTGACACCAAGGCTGG
CATTGCCCTCAATGACCACTTCGTCAAGCTCATTTCCTGGTATGACAATGAATTTGGCTACAGCAACTAGGTGGTGGACC
TCATGGTCCACATGGCCTCCAAGGAG
ORF - retro_cfam_1407 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 73.21 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MVKLGVNEFAHIGRLGTRAAFNSGKEDIVTINDSFIDLNYMVYMFQYDSTHGKFYGMVKAENGKLVINGK |
| MVK.GVN.F..IGRL.TRAAFNSGK.DIV.IND.FIDLN.MVYMFQYDSTHGKF...VKAENGKLVINGK | |
| Retrocopy | MVKVGVNGFGRIGRLVTRAAFNSGKMDIVAINDPFIDLNLMVYMFQYDSTHGKFHSTVKAENGKLVINGK |
| Parental | SISIFQERHPANNKWGDAGAEYVVEPTGVFTTMENAGAHLKSGAKRVIISAPSADAPMFVMGVNHEKYNK |
| SISIFQER.PAN.KWG.AGAEYVVE.TGVFTTME.AGAHLK.GAKRVIISAPSADAPMFVMGVNH.KY.. | |
| Retrocopy | SISIFQERDPANIKWGNAGAEYVVESTGVFTTMEKAGAHLKGGAKRVIISAPSADAPMFVMGVNHKKYDN |
| Parental | SLKIVS-NASCTTNCLAPLAKVIHDHFGIVEGLMTTAHAITATQKTMGGTSGKLWPEGRVPVQNIIPAST |
| SLKIV..NASCT.NCLA.LAKVIHDHFGI.EGLM.T.HAITATQKT..G.SGKLW..G....QNIIP... | |
| Retrocopy | SLKIVT<NASCTINCLASLAKVIHDHFGIMEGLMITVHAITATQKTVDGPSGKLWHDG*GDAQNIIP--- |
| Parental | GAATAVGKVIPELKGKFIGMAFRVPTPNMSVVDLTCPLEKAAKYDNIKKVVKQASEGPLKGIL--AEDQV |
| .A.T...K...........MAFRVPTPNMSVVDLT..LEKAAKYDNIKKVVKQASEGPLKGIL...EDQV | |
| Retrocopy | -AFTGTAKAMGKVILEAHCMAFRVPTPNMSVVDLTGRLEKAAKYDNIKKVVKQASEGPLKGILGYTEDQV |
| Parental | VSCDFNSDTHPSIFDTGAGIAFNDHLVKHSSVKYSINKFSFSSSEVEISSHIIHED |
| VSC.FNSDTH.S.FDT.AGIA.NDH.VK........N.F..S...V....H..... | |
| Retrocopy | VSCNFNSDTHSSTFDTKAGIALNDHFVK--LISWYDNEFGYSN*VVDLMVHMASKE |
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 | 0 .00 RPM |
| SRP017611_brain | 0 .00 RPM | 0 .00 RPM |
| SRP017611_kidney | 0 .00 RPM | 0 .00 RPM |
| SRP017611_liver | 0 .07 RPM | 0 .00 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_1407 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_1407 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cfam_1407 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 32 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Canis familiaris | ENSCAFG00000002325 | 1 retrocopy |
retro_cfam_1407 ,
|
| Canis familiaris | ENSCAFG00000015077 | 4 retrocopies | |
| Tupaia belangeri | ENSTBEG00000001510 | 27 retrocopies |
retro_tbel_1055, retro_tbel_1149, retro_tbel_1315, retro_tbel_1359, retro_tbel_1519, retro_tbel_1684, retro_tbel_232, retro_tbel_2380, retro_tbel_2442, retro_tbel_2731, retro_tbel_2992, retro_tbel_3109, retro_tbel_3205, retro_tbel_3418, retro_tbel_3463, retro_tbel_3826, retro_tbel_3829, retro_tbel_393, retro_tbel_4036, retro_tbel_4094, retro_tbel_4310, retro_tbel_4377, retro_tbel_441, retro_tbel_4560, retro_tbel_4635, retro_tbel_4706, retro_tbel_480,
|