RetrogeneDB ID: | retro_cjac_2878 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 7:52977035..52977593(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | DSCR3 | ||
| Ensembl ID: | ENSCJAG00000002626 | ||
| Aliases: | None | ||
| Description: | Down syndrome critical region gene 3 [Source:HGNC Symbol;Acc:3044] |
Retrocopy-Parental alignment summary:
>retro_cjac_2878
ATGGGGACAGTCCTGGACATCAAGATTAAAAGAGCAAATAAAGTTTATGACACTGGGGAGGTGCTCTCCTGTGTGGTGGT
AACATCGAGTAAAGATTCAGTCCAACACAACGGACTGACTTGGCCCATGGAAGGAACTGTAAACCTCCACCTCAATGCCA
AAAGTCTGGGTGTGTTTGAAGCTTCTTATAATTCTGTTAAGCCTATCCAGATTATCATCAGCACCATAGAAATGGTGAAG
CTGGGGAAATCTCTCAGTGGCAAAACAGAAAGCCCTTTGAGTTTCCTCTGCACATGAAGGGTAACAAAGTTCTGTGTGAG
ACTTATCATGGCACGTTTGTCAACATTCAGAACATACTATGCTATGACTCGAGGCAATCTCTGTTGGCCAAGGACTTGAC
AAAGACCTGTGAATTTATCATTCACTGTTCCTCAGAAGGGGAAGTTGACTCCCAGTCCTGTGACCTTCATGAGTACACCT
GAAACCTTATAGAACGTCAAAGAGAGAGCTCTGCTTCCCAAATTTCTCATTCGAGGACATCTCAACAATAAACTGTGT
ORF - retro_cjac_2878 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 75.66 % |
| Parental protein coverage: | 62.96 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | MGTALDIKIKRANKVYHAGEVLSGVVVISSKDSVQHQGVSLTMEGTVNLQLSAKSVGVFEAFYNSVKPIQ |
| MGT.LDIKIKRANKVY..GEVLS.VVV.SSKDSVQH.G....MEGTVNL.L.AKS.GVFEA.YNSVKPIQ | |
| Retrocopy | MGTVLDIKIKRANKVYDTGEVLSCVVVTSSKDSVQHNGLTWPMEGTVNLHLNAKSLGVFEASYNSVKPIQ |
| Parental | ILNSTIEMVKPGKFPSGKTEI-PFEFPLHVKGNKVLYETYHGVFVNIQYTLRCDMRRSLLAKDLTKTCEF |
| I..STIEMVK.GK..SGKTE..PFEFPLH.KGNKVL.ETYHG.FVNIQ..L..D.R.SLLAKDLTKTCEF | |
| Retrocopy | IIISTIEMVKLGKSLSGKTES<PFEFPLHMKGNKVLCETYHGTFVNIQNILCYDSRQSLLAKDLTKTCEF |
| Parental | IVHSAPQKGKL-TPSPVDFTITPETLQNVKERALLPKFLIRGHLNSTNC |
| I.H.....G...TPSPV.F..TPETL.NVKERALLPKFLIRGHLN...C | |
| Retrocopy | IIHCS-SEGEV>TPSPVTFMSTPETL*NVKERALLPKFLIRGHLNNKLC |
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 .00 RPM | 6 .77 RPM |
| SRP051959_heart | 0 .00 RPM | 10 .23 RPM |
| SRP051959_kidney | 0 .00 RPM | 10 .56 RPM |
| SRP051959_liver | 0 .00 RPM | 5 .65 RPM |
| SRP051959_lung | 0 .00 RPM | 10 .20 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 11 .00 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 14 .63 RPM |
| SRP051959_spleen | 0 .00 RPM | 10 .38 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2878 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2878 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2878 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 5 parental genes, and 5 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000002626 | 1 retrocopy |
retro_cjac_2878 ,
|
| Macropus eugenii | ENSMEUG00000007920 | 1 retrocopy | |
| Nomascus leucogenys | ENSNLEG00000004717 | 1 retrocopy | |
| Pan troglodytes | ENSPTRG00000013900 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000001681 | 1 retrocopy |