RetrogeneDB ID: | retro_cjac_3918 | ||
Retrocopylocation | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | GL286238.1:41028..41418(-) | ||
| Located in intron of: | None | ||
Retrocopyinformation | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | TMEM128 | ||
| Ensembl ID: | ENSCJAG00000000112 | ||
| Aliases: | None | ||
| Description: | transmembrane protein 128 [Source:HGNC Symbol;Acc:28201] |
Retrocopy-Parental alignment summary:
>retro_cjac_3918
GAAACCTCTACAGCTGTTGAGAAAAAGAGAAACCTCTTCCAAGACTTAATATCCATTCTGGATTCTGGATTTTGGCATCC
ATTGTTGTGACCTATTATGCTGACTTCTTTAATACTTTTAAAGAAAGCTTTCACACTAGCAGCTGGTTTCTCTGTGGCAG
TGCCTTGTTGTTTGTTAGTTTATCAATTGTGTTTTACTGCATAGTATACCTTGAGTGGTATCATGGAATTGGAGAATATG
ATGTCAAGCATCCAGCCCTGATTCCCATTACCACTGCTGCCTTTATTGCAGCAGGAATTTGCTGCAACATTTTTTTTATG
GCATGTGTGGTCATTTTTCACTACATTGTTGTCGTTTACCCAGTTTATGGGGGTTGTAATGTTTATCTCA
GAAACCTCTACAGCTGTTGAGAAAAAGAGAAACCTCTTCCAAGACTTAATATCCATTCTGGATTCTGGATTTTGGCATCC
ATTGTTGTGACCTATTATGCTGACTTCTTTAATACTTTTAAAGAAAGCTTTCACACTAGCAGCTGGTTTCTCTGTGGCAG
TGCCTTGTTGTTTGTTAGTTTATCAATTGTGTTTTACTGCATAGTATACCTTGAGTGGTATCATGGAATTGGAGAATATG
ATGTCAAGCATCCAGCCCTGATTCCCATTACCACTGCTGCCTTTATTGCAGCAGGAATTTGCTGCAACATTTTTTTTATG
GCATGTGTGGTCATTTTTCACTACATTGTTGTCGTTTACCCAGTTTATGGGGGTTGTAATGTTTATCTCA
ORF - retro_cjac_3918 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 89.39 % |
| Parental protein coverage: | 78.79 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | ETSTAVEKK-ERPLPRLNIHSGFWILASIIVTYYADFFKTLKESFHTSSWFLCGSALLLVSLSIAFYCIV |
| ETSTAVEKK.E.PLPRLNIHSGFWILASI.VTYYADFF.T.KESFHTSSWFLCGSALL.VSLSI.FYCIV | |
| Retrocopy | ETSTAVEKK<EKPLPRLNIHSGFWILASIVVTYYADFFNTFKESFHTSSWFLCGSALLFVSLSIVFYCIV |
| Parental | YLEWYCGIGEYDVKYPALIPITTAAFIAAGICFNI-ALWHVWSFFTPLLLFTQFMGVVMFIS |
| YLEWY.GIGEYDVK.PALIPITTAAFIAAGIC.NI..LWHVWSFFT.LL.FTQFMGVVMFIS | |
| Retrocopy | YLEWYHGIGEYDVKHPALIPITTAAFIAAGICCNI>FLWHVWSFFTTLLSFTQFMGVVMFIS |
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 .55 RPM |
| SRP051959_heart | 0 .02 RPM | 4 .72 RPM |
| SRP051959_kidney | 0 .00 RPM | 10 .83 RPM |
| SRP051959_liver | 0 .00 RPM | 5 .83 RPM |
| SRP051959_lung | 0 .00 RPM | 5 .84 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 5 .91 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 4 .91 RPM |
| SRP051959_spleen | 0 .00 RPM | 6 .16 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3918 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3918 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_3918 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Choloepus hoffmanni | ENSCHOG00000004471 | 1 retrocopy | |
| Callithrix jacchus | ENSCJAG00000000112 | 3 retrocopies |
retro_cjac_3437, retro_cjac_3717, retro_cjac_3918 ,
|