RetrogeneDB ID: | retro_cfam_1973 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | 9:15550243..15550922(+) | ||
| Located in intron of: | ENSCAFG00000010877 | ||
Retrocopy information | Ensembl ID: | ENSCAFG00000010967 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CMSS1 | ||
| Ensembl ID: | ENSCAFG00000009230 | ||
| Aliases: | CMSS1, C33H3orf26 | ||
| Description: | cms1 ribosomal small subunit homolog (yeast) [Source:HGNC Symbol;Acc:28666] |
Retrocopy-Parental alignment summary:
>retro_cfam_1973
TGTGGCCTCATCAAGATTTCTGTTTCCACAAAAGAAGATGTCACCAAGACAAGGAGGAGAAGAAAGAAGAAAATTACTGA
TGTTCTTGCAAAATCAGAGCCAAAACCGGGGACCCCTGAAGACCTGCAGAACTTGATGAAGGACTATTTCAGCAGCAGCC
GCTCAGTGATTGAATTAGAAGAACTAAACCTACCAGACTCCTGTTTCCTCAAGGCCAATGATTTGACTCATAGTCTTTCA
TCATACCTAAGAGAAATCTGCCCTAAGTGGGTAAAACTTCGGAAAAACCATAATGAGAAGAAATCGGTTCTGATGCTGAT
CATCTGCAGCTCTGCTGTCCGGGCCTTGGAGCTCATTAGGTCGATGACAGCATTCAGAGGAGACAGCAAAGTTATGAAAT
TATTTGCAAAACACATAAAGGTCCAGGAGCAGGTAAAGCTGCTGGGGAAGCGTGTTGTACACCTGGGTGTAGGAACACCA
GGGAGGATTAAAGAACTCATTAAACAAGGTGGCCTTAATTTGAACCCCTTAAAGTTCCTGGTTTTTGACTGGAACTGGAG
AGATCAGAAGTTGAGGAGGATGATGGACATTCCTGAGATTAGAAAGGAGGTTTTTGAACTTCTGGAAATGGGAGTCCTCA
AGTCTGTGCAAATCAGAATCTTTGAAGCTGGGCCTTTTC
ORF - retro_cfam_1973 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 96.48 % |
| Parental protein coverage: | 81.52 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | CFLIKPK-ETKEDATKTRRRRKKKITDVLAKSEPKPGTPEDLQNLMKDYFSSSRSVIELEELNLPDSCFL |
| C.LIK....TKED.TKTRRRRKKKITDVLAKSEPKPGTPEDLQNLMKDYFSSSRSVIELEELNLPDSCFL | |
| Retrocopy | CGLIKISVSTKEDVTKTRRRRKKKITDVLAKSEPKPGTPEDLQNLMKDYFSSSRSVIELEELNLPDSCFL |
| Parental | KANDLTHSLSSYLREICPKWVKLRKNHNEKKSVLMLIICSSAVRALELIRSMTAFRGDSKVMKLFAKHIK |
| KANDLTHSLSSYLREICPKWVKLRKNHNEKKSVLMLIICSSAVRALELIRSMTAFRGDSKVMKLFAKHIK | |
| Retrocopy | KANDLTHSLSSYLREICPKWVKLRKNHNEKKSVLMLIICSSAVRALELIRSMTAFRGDSKVMKLFAKHIK |
| Parental | VQEQVKLLEKRVVHLGVGTPGRIKELIKQGGLNLNPLKFLVFDWNWRDQKLRRMMDIPEIRKEVFELLEM |
| VQEQVKLL.KRVVHLGVGTPGRIKELIKQGGLNLNPLKFLVFDWNWRDQKLRRMMDIPEIRKEVFELLEM | |
| Retrocopy | VQEQVKLLGKRVVHLGVGTPGRIKELIKQGGLNLNPLKFLVFDWNWRDQKLRRMMDIPEIRKEVFELLEM |
| Parental | GVL-SLCKSESLKLGLF |
| GVL.SLCKSESLKLGLF | |
| Retrocopy | GVL>SLCKSESLKLGLF |
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 .04 RPM | 9 .62 RPM |
| SRP017611_brain | 0 .00 RPM | 13 .26 RPM |
| SRP017611_kidney | 0 .00 RPM | 4 .49 RPM |
| SRP017611_liver | 0 .00 RPM | 2 .54 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_1973 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_1973 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cfam_1973 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Canis familiaris | ENSCAFG00000009230 | 1 retrocopy |
retro_cfam_1973 ,
|
| Mustela putorius furo | ENSMPUG00000011324 | 2 retrocopies | |
| Ochotona princeps | ENSOPRG00000002986 | 1 retrocopy |