RetrogeneDB ID: | retro_cjac_1750 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 19:33184030..33184453(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSCJAG00000015321 | ||
| Aliases: | None | ||
| Description: | U1 small nuclear ribonucleoprotein C [Source:UniProtKB/TrEMBL;Acc:F6XG37] |
Retrocopy-Parental alignment summary:
>retro_cjac_1750
TATACTTCACCCATGACTCCATCTGTGAGAAAGACACACTGCAGTGGTAGGAAACACAAAGAGAAGGTGAAAGACGACTA
TCAGAAATGGATGGAAGAGCAGGCTCAGAGCCTGATTCACACAACAACAGCTGCATTTCCACAAGGAAAGATACCTCCTA
CTCCATTCTCTGCTCCTCCTCCTGCAGGGGCGATGAAACCATCTCCCCCAAGTCTTCCGGGTCCTCCTCGCCCTGGGATG
ATGCCAGCACCCCATATGGGGGGCCCTCCGCCTCCTGGGATGATGCCAGTGGGACCTGCTCCTGGAATGAGGCCACCCAT
GGGAGGCCATATGCCAATGATGCCTGGGCCCCCAATGATGAGAACTGCCCGTCCCATGATGGTGCCCATTCGGCCTGGAA
TGACTCGACCAGACAGATAAGGA
ORF - retro_cjac_1750 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 69.23 % |
| Parental protein coverage: | 89.31 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | YLTHDSPSVRKTHCSGRKHKENVKDYYQKWMEEQAQSLIDKTTAAFQQGKIPPTPFSAPPPAGAMIPPPP |
| Y.....PSVRKTHCSGRKHKE.VKD.YQKWMEEQAQSLI..TTAAF.QGKIPPTPFSAPPPAGAM.P.PP | |
| Retrocopy | YTSPMTPSVRKTHCSGRKHKEKVKDDYQKWMEEQAQSLIHTTTAAFPQGKIPPTPFSAPPPAGAMKPSPP |
| Parental | SLPGPPRPGMMPAPHMGGPPMMPMMG-PPPPGMMPVGPAPGMRPPMGGHMPMMPGPPMMRPPARPMMVPT |
| SLPGPPRPGMMPAPHMGGPP...MM...P.PGM.P..P..G..P.M.G...M....PMM.P....M..P. | |
| Retrocopy | SLPGPPRPGMMPAPHMGGPPPPGMMPVGPAPGMRP--PMGGHMPMMPGPPMMRTARPMMVPIRPGMTRPD |
| Parental | RPG |
| R.G | |
| Retrocopy | R*G |
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 | 1 .42 RPM | 8 .36 RPM |
| SRP051959_heart | 1 .23 RPM | 8 .61 RPM |
| SRP051959_kidney | 1 .93 RPM | 8 .43 RPM |
| SRP051959_liver | 1 .60 RPM | 8 .53 RPM |
| SRP051959_lung | 1 .85 RPM | 9 .89 RPM |
| SRP051959_lymph_node | 1 .85 RPM | 8 .97 RPM |
| SRP051959_skeletal_muscle | 1 .75 RPM | 12 .51 RPM |
| SRP051959_spleen | 1 .51 RPM | 9 .31 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1750 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1750 was not experimentally validated.