RetrogeneDB ID: | retro_cjac_1981 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 2:186033800..186034375(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000011821 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | AURKAIP1 | ||
| Ensembl ID: | ENSCJAG00000034618 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_1981
ATACTCCGGGTGCGCCTGACTTCTCAGCTGCTCAAGGCTGTTTCCTGGGCAGGCTGCAGTCCGCCCTGGCCTGTCTCGGG
AGTGCTGGGCAGCCATACCTGCAGGCCCCCTTACAGCACACAGCCAGCTGGCACAGGTAGGGCTGCCTCCCTCCTTGGAA
AGGGGGCCCAGCTGGAGCTCGAGGAGATGCTGGTCCCCAGGAAGATGTCCACCAGCCCCCTGGAGAGCTGCCTTACAGCC
CGCTGCCTCCTGCTCAGACTGGATGCCCGGACTACGGGGACTGCGGCTCCAGCCCAATTCTATGAGTGTCCGCATAGCCC
AATGGGGGAAGGGGCCAAGCAGGGGGATGAAAAGGTCTGGGATGCACCTCAGATGCAGCGCAAACACGTGTTGAAGACTC
GCAGGCGGAAGATGAACCACCACAAGTACCGGAAGGGGCAGAGAGGCCCCCGGTTCCTGCAGCGGAAGTTCCGGGAAGGA
CTTAAGCAGATCACGTTCAAAAGAGACCAGAGGCGCGTCTGGCTGAAGGAAACCCCTGAGCCTGTCAGACCTCCCGGGTC
TACCTGAGGGGCAGA
ORF - retro_cjac_1981 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 65.0 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MLLVRLTSPLFRAVPWAGCRRLWPSSGELGGRACGHFYSTQPAGRGRTASLPRKGAQLELEEMLVPRKMS |
| .L.VRLTS.L..AV.WAGC...WP.SG.LG...C...YSTQPAG.GR.ASL..KGAQLELEEMLVPRKMS | |
| Retrocopy | ILRVRLTSQLLKAVSWAGCSPPWPVSGVLGSHTCRPPYSTQPAGTGRAASLLGKGAQLELEEMLVPRKMS |
| Parental | ISPLESWLTARCLLPRLDSGTPGTVAPPQPHECPPCHTGEGAEQGDEGVGDAPVMQCKNVLKIRRRKMNH |
| .SPLES.LTARCLL.RLD..T.GT.AP.Q..ECP....GEGA.QGDE.V.DAP.MQ.K.VLK.RRRKMNH | |
| Retrocopy | TSPLESCLTARCLLLRLDARTTGTAAPAQFYECPHSPMGEGAKQGDEKVWDAPQMQRKHVLKTRRRKMNH |
| Parental | HKYRKLVKRTRFLRRKIREGRLKRKQLKFERDLRRIWLKAGLKEAPE-GWQTPKIYQRGR |
| HKYRK.....RFL.RK.REG....KQ..F.RD.RR.WLK....E.PE...QT...Y.RGR | |
| Retrocopy | HKYRKGQRGPRFLQRKFREG---LKQITFKRDQRRVWLK----ETPE<ACQTSRVYLRGR |
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 | 2 .91 RPM |
| SRP051959_heart | 0 .00 RPM | 4 .35 RPM |
| SRP051959_kidney | 0 .00 RPM | 4 .57 RPM |
| SRP051959_liver | 0 .00 RPM | 6 .93 RPM |
| SRP051959_lung | 0 .02 RPM | 3 .16 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 3 .36 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 10 .96 RPM |
| SRP051959_spleen | 0 .00 RPM | 2 .46 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1981 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1981 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_1981 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000034618 | 1 retrocopy |
retro_cjac_1981 ,
|
| Myotis lucifugus | ENSMLUG00000004317 | 1 retrocopy | |
| Tursiops truncatus | ENSTTRG00000017044 | 1 retrocopy |