RetrogeneDB ID: | retro_cjac_2485 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 4:149158376..149158636(-) | ||
| Located in intron of: | ENSCJAG00000019537 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | LYRM2 | ||
| Ensembl ID: | ENSCJAG00000000905 | ||
| Aliases: | None | ||
| Description: | LYR motif containing 2 [Source:HGNC Symbol;Acc:25229] |
Retrocopy-Parental alignment summary:
>retro_cjac_2485
ATGGCCGCCTCCCACTTACCCTCAGCCATGCTAACATTAAAGCAGTTCATAAGAAGGCAACAAGTTCTTCTCTACAGAAG
GATTTTGCAAACAATTTGGCAAATTCCAAATGATTCTGATCGCAATTAACAGAAGGATTGGGCAAGGGAAGAATTCAGAA
GAAACAAAGTGCCACCGAAGAGGGCACAGTCCTGATGCTGATTACTCAAGGCAATATTGCAGCTCAAGGAGTTAGAAAAA
CACTTGCTTTAGCAAAATCT
ORF - retro_cjac_2485 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 79.12 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | MAATRLPPATLTLKQFIRRQQVLLLYRRILQTIRQVPNDSDRKYLKDWAREEFKRNK-SATEEDTIRMMI |
| MAA..LP.A.LTLKQFIRRQQV.LLYRRILQTI.Q.PNDSDR...KDWAREEF.RNK.SATEE.T..M.I | |
| Retrocopy | MAASHLPSAMLTLKQFIRRQQV-LLYRRILQTIWQIPNDSDRN*QKDWAREEFRRNK<SATEEGTVLMLI |
| Parental | TQGN-MQLKELE-KTLALAKS |
| TQGN..QLKELE.KTLALAKS | |
| Retrocopy | TQGN>LQLKELE<KTLALAKS |
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 |
|---|---|---|
| SRP051959_colon | 0 .13 RPM | 1 .71 RPM |
| SRP051959_heart | 0 .11 RPM | 1 .96 RPM |
| SRP051959_kidney | 0 .02 RPM | 3 .57 RPM |
| SRP051959_liver | 0 .09 RPM | 2 .71 RPM |
| SRP051959_lung | 0 .13 RPM | 1 .97 RPM |
| SRP051959_lymph_node | 0 .05 RPM | 1 .62 RPM |
| SRP051959_skeletal_muscle | 0 .07 RPM | 2 .51 RPM |
| SRP051959_spleen | 0 .21 RPM | 2 .10 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2485 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2485 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2485 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 4 parental genes, and 7 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000000905 | 1 retrocopy |
retro_cjac_2485 ,
|
| Cavia porcellus | ENSCPOG00000015625 | 4 retrocopies | |
| Homo sapiens | ENSG00000083099 | 1 retrocopy | |
| Macropus eugenii | ENSMEUG00000009916 | 1 retrocopy |