RetrogeneDB ID: | retro_cfam_842 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | 19:18833983..18834600(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | SCCPDH | ||
| Ensembl ID: | ENSCAFG00000015884 | ||
| Aliases: | None | ||
| Description: | saccharopine dehydrogenase (putative) [Source:HGNC Symbol;Acc:24275] |
Retrocopy-Parental alignment summary:
>retro_cfam_842
ATTGTTGGTCCAAAATTGAAAAGAAGGTGGCCAATTTTTTACCGCAGAGAACTGAATAGCTATTCTATTCCTTTCTTGGG
AGCAGATGTCTCTGTTGTGAGGCGGACTCAGCGTTACTTGCATGAGAATTTGGAGCAATCGCCTGTTCAGTGAGCCGCTT
ACTGACTGTGGGAGGCATCACCTCCGTTATTAAGCTGATGTTTGCAGGACTTTTCTTTTTATTCTTTGTGAAGTGTGGCA
TTGGCAGGCAGCTTCTCATAAAATTTCCATGGCTCTTCTCCTTTGGTTATTTTTCAAAACAAGGTCCAACACAAAAACAG
ATGGATGCCGCCTCGTTTACAATGACATTCTTTGGTCAAGGATACAGTCAAGGCTTTGGTCTGGAGAAGAACAAACCAAA
TATGAGAATTTGTACTCAGGTGAAAGGACCAGAGGCTGGCTACGTGGCTACCCCCATAGCCATGGTCCAGGCAGCCATGA
CCCTTCTAAACGATACCTCTGATCTTCCTAACAGGGGCGGGGTCTTCACACCTGGAGCAGCCTTCTGCAGAACAAAGTTG
ATTGACAGACTCAATCAACCTGGCATTGAATTTAGTGTCATTAGCAGCTCTGAAGTC
ORF - retro_cfam_842 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 96.14 % |
| Parental protein coverage: | 53.51 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | IVGPKLKRRWPISYCRELNSYSIPFLGADVSVVRRTQRYLHENLEQSPVQYAAY-VTVGGITSVIKLMFA |
| IVGPKLKRRWPI.Y.RELNSYSIPFLGADVSVVRRTQRYLHENLEQSPVQ.AAY..TVGGITSVIKLMFA | |
| Retrocopy | IVGPKLKRRWPIFYRRELNSYSIPFLGADVSVVRRTQRYLHENLEQSPVQ*AAY<LTVGGITSVIKLMFA |
| Parental | GLFFLFFVKCGIGRQLLIKFPWLFSFGYFSKQGPTQKQMDAASFTMTFFGQGYSQGFGPEKNKPNMRICT |
| GLFFLFFVKCGIGRQLLIKFPWLFSFGYFSKQGPTQKQMDAASFTMTFFGQGYSQGFG.EKNKPNMRICT | |
| Retrocopy | GLFFLFFVKCGIGRQLLIKFPWLFSFGYFSKQGPTQKQMDAASFTMTFFGQGYSQGFGLEKNKPNMRICT |
| Parental | QVKGPEAGYVATPIAMVQAAMTLLNDTSDLPNTGGVFTPGAAFCRTKLIDRLNQRGIEFSVISSSEV |
| QVKGPEAGYVATPIAMVQAAMTLLNDTSDLPN.GGVFTPGAAFCRTKLIDRLNQ.GIEFSVISSSEV | |
| Retrocopy | QVKGPEAGYVATPIAMVQAAMTLLNDTSDLPNRGGVFTPGAAFCRTKLIDRLNQPGIEFSVISSSEV |
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 .13 RPM | 55 .86 RPM |
| SRP017611_brain | 0 .08 RPM | 59 .94 RPM |
| SRP017611_kidney | 70 .79 RPM | 164 .96 RPM |
| SRP017611_liver | 0 .15 RPM | 58 .45 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_842 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_842 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cfam_842 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 | ENSCAFG00000015884 | 1 retrocopy |
retro_cfam_842 ,
|
| Dasypus novemcinctus | ENSDNOG00000016354 | 1 retrocopy | |
| Monodelphis domestica | ENSMODG00000006356 | 1 retrocopy |