RetrogeneDB ID: | retro_cfam_753 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | 17:25540866..25541465(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | C11orf84 | ||
| Ensembl ID: | ENSCAFG00000015053 | ||
| Aliases: | None | ||
| Description: | chromosome 11 open reading frame 84 [Source:HGNC Symbol;Acc:25115] |
Retrocopy-Parental alignment summary:
>retro_cfam_753
CTGAAGGCCGAGGGCGCCGCGCTCGACTGCTTCGAGGTGACGCTCAAAAGCGAGGAAGGGGAGGACGAGGCAGAGGCCGT
GGTGGTGGCCGCAATTCCACGGCCCGAGCCGATGCTCAGAGTGGCCCAGCAGGAGAAGACCCCACCGCCGAGGCCCAGCC
TGCTGGAGGCAGGCAGCCGTGGCTGTGAGGAGCCCAAGCAGCAGGTGTCTTGGGAGCAGGAGTTCCTTGCGGGAAACAGC
CCCGGAGGCAGCGGGCGGGCACTGTGCATGGTGCGTGGGTCCGAAATCCGGCCCCCCCTGCCGACACGGCGCGCATGCAT
ACCCTGGAGCAGCGGCCTCACAGCCTGGACCTGAGCCCTTCAGGGAAAAGCAACATCCTGGAGGCCTGGAGTGAGGGAGC
GGCCCATTTGCAAGACATCAGAGCTGAGCAGCCTTCCTCGCCCACCTCAGACTCAGGCCAGGATGTGGAAGCTGACCCGG
GCTCCGACCCAGACCCTGCCTAAACGCCAGCAGAGATCGCGGTTCTCCTCGACTCTGAGGACAACCCATCTCTCCCGAAA
AGGAGCCGGCCCAGGGGACTCCGCCCCCTCGAGCTTCCT
ORF - retro_cfam_753 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 90.05 % |
| Parental protein coverage: | 94.79 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | LKAEGAALDCFEVTLKCEEGEDEEEAVVVAVIPRPEPMLRVAQQEKTPPPRPNLLEAGSDGCEEPKQQVS |
| LKAEGAALDCFEVTLK.EEGEDE.EAVVVA.IPRPEPMLRVAQQEKTPPPRP.LLEAGS.GCEEPKQQVS | |
| Retrocopy | LKAEGAALDCFEVTLKSEEGEDEAEAVVVAAIPRPEPMLRVAQQEKTPPPRPSLLEAGSRGCEEPKQQVS |
| Parental | WEQEFLVGNSPGGSGRALCMVCGSEIR-SPSADTARMHILEQHPHTLDLSPSEKSNILEAWSEGVALLQD |
| WEQEFL.GNSPGGSGRALCMV.GSEIR..P.ADTARMH.LEQ.PH.LDLSPS.KSNILEAWSEG.A.LQD | |
| Retrocopy | WEQEFLAGNSPGGSGRALCMVRGSEIR<APPADTARMHTLEQRPHSLDLSPSGKSNILEAWSEGAAHLQD |
| Parental | IRAEQPSSPTSDSGQDVEADPDSDPDPAKMPAEIVVLLDSEDNPSLPKRSRPRGLRPLELP |
| IRAEQPSSPTSDSGQDVEADP.SDPDPA..PAEI.VLLDSEDNPSLPKRSRPRGLRPLELP | |
| Retrocopy | IRAEQPSSPTSDSGQDVEADPGSDPDPA*TPAEIAVLLDSEDNPSLPKRSRPRGLRPLELP |
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 .42 RPM | 7 .14 RPM |
| SRP017611_brain | 0 .56 RPM | 6 .99 RPM |
| SRP017611_kidney | 0 .07 RPM | 1 .65 RPM |
| SRP017611_liver | 0 .00 RPM | 0 .51 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_753 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_753 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cfam_753 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Canis familiaris | ENSCAFG00000015053 | 1 retrocopy |
retro_cfam_753 ,
|
| Callithrix jacchus | ENSCJAG00000018418 | 1 retrocopy |