RetrogeneDB ID: | retro_cjac_2674 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 5:139101416..139101863(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | EMD | ||
| Ensembl ID: | ENSCJAG00000011853 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_2674
GTGGATTCAGATATGTATGATCTTCCCAAGAAAGAGGACGCCTTACTCTACCAGAGCAAGGGCTACAGTGACGACTACTA
TGAAGAGAGCTACTTAACTACCAGGATTTATGGGGAGCCCGACTCTGCGGGCCAGTCCAGGGGCTTCCACCAGTCTGCGA
CTTCACTCCCAGATGCTGACACTTTCCATCACCAGGTGCGTGATGACAATCTTTTGTCGTCTTCTGAAGAGGAGTGCGAG
GATAGGGAATGCCCCATGTGCGGCTGGGACAGTGGCTACCAGAGCATCGCAGACTACCGCCCTGTTTCATCCTCCAGGAG
CTCCCTGGGCCTGTCCTATTATCCTACCTCCTCCACCTCTTCTGTGTCCTAATCATCTTCCCCTTCATGGCTTACCCGCC
GAGGCATCCGGCCAGAAAAGCATGCTCCTGGGGCCGGGCTTGGCCAC
ORF - retro_cjac_2674 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 90.07 % |
| Parental protein coverage: | 58.82 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | VDSDMYDLPKKEDALLYQSKGYNDDYYEESYLTTRTYGEPDSAGQSRGFRQSATSLPDADTFHHQVRDDN |
| VDSDMYDLPKKEDALLYQSKGY.DDYYEESYLTTR.YGEPDSAGQSRGF.QSATSLPDADTFHHQVRDDN | |
| Retrocopy | VDSDMYDLPKKEDALLYQSKGYSDDYYEESYLTTRIYGEPDSAGQSRGFHQSATSLPDADTFHHQVRDDN |
| Parental | LLSS-EEECKDRERPMYGRDSAYQSIAHYRPVSASRSSLGLSYYPTSSSTSSVSSSSSSPSWLTRRAIRP |
| LLSS.EEEC.DRE.PM.G.DS.YQSIA.YRPVS.SRSSLGLSYYPT.SSTSSV.S.SSSPSWLTRR.IRP | |
| Retrocopy | LLSSSEEECEDRECPMCGWDSGYQSIADYRPVSSSRSSLGLSYYPT-SSTSSV-S*SSSPSWLTRRGIRP |
| Parental | EKHAPGAGLGH |
| EKHAPGAGLGH | |
| Retrocopy | EKHAPGAGLGH |
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 | 5 .52 RPM |
| SRP051959_heart | 0 .07 RPM | 5 .37 RPM |
| SRP051959_kidney | 0 .07 RPM | 4 .19 RPM |
| SRP051959_liver | 0 .02 RPM | 3 .44 RPM |
| SRP051959_lung | 0 .03 RPM | 5 .35 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 5 .82 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 5 .28 RPM |
| SRP051959_spleen | 0 .00 RPM | 4 .87 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2674 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2674 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2674 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 | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000011853 | 1 retrocopy |
retro_cjac_2674 ,
|
| Tursiops truncatus | ENSTTRG00000013924 | 1 retrocopy |