RetrogeneDB ID: | retro_cfam_1201 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | 26:33138826..33139370(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CA5B | ||
| Ensembl ID: | ENSCAFG00000012150 | ||
| Aliases: | None | ||
| Description: | carbonic anhydrase VB, mitochondrial [Source:HGNC Symbol;Acc:1378] |
Retrocopy-Parental alignment summary:
>retro_cfam_1201
ATCGATGCTTGGGGCTCTGAGCATACTGTGGACAGCAAATGTTACCCGGCAGAGCTGCACTTGGTGCATTGGAATGCAGT
CAAATTTGAAAACTTTGAGGATGCAGCACTAGAAGAACATGGTTTGGCTGTAATAGTATTTTTAAAGTTAGGCAAACATC
ACCAAGAACTACAGAAATCGGTGGATACCTTGCCATCAGTCAAGCATAAGGACACCCTTGTGGCATTTGGGTCATTCGAT
CCTTCCTGCCTGATGCCTGCCTGCCCAGATTACTGGACCTACTCGGGGTCCCTGACTACCCCTCCACTCTCTGAGTCTGT
CACCTGGATCATTAAGAAGCAGCCCATAGAGGTTGATCATGATCAGCTTGAGCAGTTTCGGACTCTGCTTTTCACATCAG
AGGGGGAGAAGGAGAAAAGAATGGTGGACAATTTCCACCCCCTCCAGCCCCTGATGAATCGCACTGTCCGCTCTTCCTTC
CGTCATGATTATGTACTGAATAATACAAGCGAAACCCCAGTCTTCAACTAGCCAAGTGACCCCC
ORF - retro_cfam_1201 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 96.17 % |
| Parental protein coverage: | 57.41 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | IDAWGSEHTVDSKCYPAELHLVHWNAVKFENFEDAALEEHGLAVIGVFLKLGKHHQELQKLVDTLPSIKH |
| IDAWGSEHTVDSKCYPAELHLVHWNAVKFENFEDAALEEHGLAVI.VFLKLGKHHQELQK.VDTLPS.KH | |
| Retrocopy | IDAWGSEHTVDSKCYPAELHLVHWNAVKFENFEDAALEEHGLAVI-VFLKLGKHHQELQKSVDTLPSVKH |
| Parental | KDTLVEFGSFDPSCLMPACPDYWTYSGSLTTPPLSESVTWIIKKQPVEVDHDQLEQFRTLLFTSEGEKEK |
| KDTLV.FGSFDPSCLMPACPDYWTYSGSLTTPPLSESVTWIIKKQP.EVDHDQLEQFRTLLFTSEGEKEK | |
| Retrocopy | KDTLVAFGSFDPSCLMPACPDYWTYSGSLTTPPLSESVTWIIKKQPIEVDHDQLEQFRTLLFTSEGEKEK |
| Parental | RMVDNFRPLQPLMNRTVRSSFRHDYVLN-IQAKPQSSTSQVTP |
| RMVDNF.PLQPLMNRTVRSSFRHDYVLN.IQAKPQSSTSQVTP | |
| Retrocopy | RMVDNFHPLQPLMNRTVRSSFRHDYVLN>IQAKPQSSTSQVTP |
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 | 1 .47 RPM |
| SRP017611_brain | 0 .16 RPM | 1 .59 RPM |
| SRP017611_kidney | 0 .00 RPM | 2 .77 RPM |
| SRP017611_liver | 0 .00 RPM | 0 .15 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_1201 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_1201 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cfam_1201 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 | ENSCAFG00000012150 | 1 retrocopy |
retro_cfam_1201 ,
|
| Callithrix jacchus | ENSCJAG00000004353 | 1 retrocopy |