RetrogeneDB ID: | retro_cfam_1516 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | 33:1481777..1482573(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ACD | ||
| Ensembl ID: | ENSCAFG00000020352 | ||
| Aliases: | None | ||
| Description: | adrenocortical dysplasia homolog (mouse) [Source:HGNC Symbol;Acc:25070] |
Retrocopy-Parental alignment summary:
>retro_cfam_1516
TCCATTCTGATGTTGACAGGCCCTTGCACAGCGCCCCCCACTCACCCGCTGGGCCTCCACCCGCTATAGGGCTGCGGGAG
AAGCTGTGTACACTGTCCCCAGCTCCTGGCTGCACATCTCGGAGAATGACCAGCGAGTTCTGAGCTCTCTGGGCCCAGGC
CCCAGGGCCCAGGCTCCAGAGCTGCCCCCACCAGACCCAGCTTTGCAGGACCTATCGCTGACTATCATCTCTCCTTCCTC
ACCTACTTCCTCAGGAACCCCAGCTTTACCCAGCCACGTGTCCTCAGAGGAAAGTGGTGCCAGCATCAGCCTTCTGCCTG
CCCTGTCCTTGGCAGCTTCAGACCTAGTGCAGAAGAGCAGCTCCCAGGCTGTACCAGCCATCTGTTCAGCCCATGGCCCC
CTGCCCCCTGGCTCCCCACACTCTAACCCTGTACCCAGTTCCCCACTCCTGAGCTGCACCCCAAGTCTGTCATCCCTTGG
CCATGTATCCAGCCCACATCAGGCCACTGTGACCAAGGCCCAGAAACCCAGCCTGGAGTTCAAGGAGCTAGGGTTGCCCC
TCAAGAACTGGCATCACTCTCCAAGGACAAAAAACGCCACAGGAGCCCTGGAATCCAGTCCCGTTTGGGACCCTCCAAAG
AGGCATCGTGATGGTTCCGCCTTCCAGTATGAGTACGAGCCACCCTGCACCTCCCTGTGTGCCCAAGTCCAAGCTGTCAG
GCTTCCTCCCCAGCTCGTGGCCTGGGCCTTGCACTTTCTGATGGAGCCACAGCCGGAGTCTGAGCTAACCCAGGTG
ORF - retro_cfam_1516 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 91.35 % |
| Parental protein coverage: | 50.96 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | SCLMLTGPCTAPP-LTRWASTRCRATGEAVYTVPSSWLHISENDQRVLSSLGPGSRTQAPELPPPDPALQ |
| S.LMLTGPCTAPP.LTRWASTR.RA.GEAVYTVPSSWLHISENDQRVLSS...........LPPPDPALQ | |
| Retrocopy | SILMLTGPCTAPP>LTRWASTRYRAAGEAVYTVPSSWLHISENDQRVLSSXXXXXXXXXXXLPPPDPALQ |
| Parental | DLSLTIVSPSSPTSSGTPALPSHVSSEENGASISLLPALSLAASDLVQKGSSQAVPAICSAHGPLPPGSP |
| DLSLTI.SPSSPTSSGTPALPSHVSSEE.GASISLLPALSLAASDLVQK.SSQAVPAICSAHGPLPPGSP | |
| Retrocopy | DLSLTIISPSSPTSSGTPALPSHVSSEESGASISLLPALSLAASDLVQKSSSQAVPAICSAHGPLPPGSP |
| Parental | HSNPVPSSPLLSCTPSLSPLGHVPSPHQAIVTKAQKPSLEFKELGLPLKNWHQSPRTKNATGALESSPVW |
| HSNPVPSSPLLSCTPSLS.LGHV.SPHQA.VTKAQKPSLEFKELGLPLKNWH.SPRTKNATGALESSPVW | |
| Retrocopy | HSNPVPSSPLLSCTPSLSSLGHVSSPHQATVTKAQKPSLEFKELGLPLKNWHHSPRTKNATGALESSPVW |
| Parental | DPPKRHRDGSAFQYEYEPPCTSLCAQVQAVKLPPQLVAWALHFLMEPQPESELTQV |
| DPPKRHRDGSAFQYEYEPPCTSLCAQVQAV.LPPQLVAWALHFLMEPQPESELTQV | |
| Retrocopy | DPPKRHRDGSAFQYEYEPPCTSLCAQVQAVRLPPQLVAWALHFLMEPQPESELTQV |
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 .34 RPM | 27 .47 RPM |
| SRP017611_brain | 0 .16 RPM | 11 .27 RPM |
| SRP017611_kidney | 0 .13 RPM | 7 .86 RPM |
| SRP017611_liver | 0 .07 RPM | 5 .22 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_1516 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_1516 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cfam_1516 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Canis familiaris | ENSCAFG00000020352 | 1 retrocopy |
retro_cfam_1516 ,
|