RetrogeneDB ID: | retro_cjac_1566 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 17:63166982..63167540(+) | ||
| Located in intron of: | ENSCJAG00000011778 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | IFT27 | ||
| Ensembl ID: | ENSCJAG00000013961 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_1566
ATGGTGAAGCTGGCAGCCAAATGCATCCTGGCAGGAGACCCAGCAGTGGGCAAGAGCACCCTGGCCCAGATCTTCCACAG
TGACGGAGCCCATTTCCAGAAGAGCTATACACTGACAACAGGAATGGATTTGGTGGTAAAGACAGTGCCAGTTCCTGACA
CAGGAGACAGTGTGGAACTCTTCATTTTTGACTCTGCTGGCAAGGAGCTGTTTTCGGAAATGCTGGATAAATTGTGGGAG
AGTCCCAACGTCTTCTGTCTCGTCTATGATGTGACCAATGAACAGTGCTTCAACAACTGCAGCAAGTGGCTGGAGAAGGC
TCGGTCACAGGCTCCAGGCATCTGTCTCCCACGTGTTTTAGTTGGGAACAAGACAGACCTGGTCAGCAGACAATAAGTGG
ACTCCGCTGAGGCCCGGGCGTGGGCGCTGGGCCAGGGCCTTGAATGCTTTGAAACATCCCTGAAGGAGATGGAAAACTTT
GAAGGCCCTTTCCACTGCCTGGACAAGCATTTCCAACAGCTGTACCGGGAGAAGATGGAGGTTTTCTGGGCACTGGTG
ORF - retro_cjac_1566 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 85.48 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MVKLAAKCILAGDPAVGKTALAQIFCSDGAHFQKSYTLTTGIDLVVKTVPVPDTGDSVEFFIFDSAGKEL |
| MVKLAAKCILAGDPAVGK..LAQIF.SDGAHFQKSYTLTTG.DLVVKTVPVPDTGDSVE.FIFDSAGKEL | |
| Retrocopy | MVKLAAKCILAGDPAVGKSTLAQIFHSDGAHFQKSYTLTTGMDLVVKTVPVPDTGDSVELFIFDSAGKEL |
| Parental | FSEMLDKLWENPNVLCLVYDVTSEQSFSNCSKWLEKARSQAPGICLPGVLVGNKTDLASRQAVDSTEARA |
| FSEMLDKLWE.PNV.CLVYDVT.EQ.F.NCSKWLEKARSQAPGICLP.VLVGNKTDL.SRQ.VDS.EARA | |
| Retrocopy | FSEMLDKLWESPNVFCLVYDVTNEQCFNNCSKWLEKARSQAPGICLPRVLVGNKTDLVSRQ*VDSAEARA |
| Parental | WALGQGLEFFETSVKELEDFKAPFHCLAEQFHQLYREKLKVFQALV |
| WALGQGLE.FETS.KE.E.F..PFHCL...F.QLYREK..VF.ALV | |
| Retrocopy | WALGQGLECFETSLKEMENFEGPFHCLDKHFQQLYREKMEVFWALV |
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 .80 RPM | 1 .24 RPM |
| SRP051959_heart | 0 .51 RPM | 2 .33 RPM |
| SRP051959_kidney | 0 .53 RPM | 2 .35 RPM |
| SRP051959_liver | 0 .32 RPM | 1 .82 RPM |
| SRP051959_lung | 1 .01 RPM | 2 .59 RPM |
| SRP051959_lymph_node | 0 .98 RPM | 1 .23 RPM |
| SRP051959_skeletal_muscle | 0 .15 RPM | 3 .58 RPM |
| SRP051959_spleen | 0 .99 RPM | 2 .29 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1566 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1566 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_1566 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 | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000026657 | 1 retrocopy | |
| Callithrix jacchus | ENSCJAG00000013961 | 1 retrocopy |
retro_cjac_1566 ,
|