RetrogeneDB ID: | retro_cjac_2047 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 21:34118972..34119389(-) | ||
| 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: | ENSCJAG00000021388 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_2047
GCCCAGCTTAACACTGGCAATGCTTTCCCTGTGGGCACCAGACCTGAGGGTATGATCATGTGCTGCGTGGTAGAGAAGCC
TAGAGACCATGGCAAGCTAACCCAGAGATCAGAGAACTATGCCATGCTTCTTTCTTACAACCCTGAGACCAAAAAGACCC
ATGCAAAGCTTCCCCTTGGTTCCACGATGCTTATCTCATCAGCCAACAGAGTTGTGGTTGGTGTGGTGGCTGGAGGTGAC
TGAACTGACAAACCCATCTTGAAGGCTGGCTGGGCCTACCACAAATATAAGGCAAAAAGGAACTTCTGGCCACGAGTATG
GGGTGCAAACACGAACCCTGTGGAGCTTCGTGTCAGAGGTGGCAACCACCAGCACATTAGCAAGCCCTTCACCATCTGCA
GAGATGCCTCTACTGGC
ORF - retro_cjac_2047 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 69.06 % |
| Parental protein coverage: | 54.09 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | AQLNIGNVLPVGTMPEGTIVCCLEEKPGDRGKLARASGNYATVISHNPETKKTRVKLPSGSKKVISSANR |
| AQLN.GN..PVGT.PEG.I.CC..EKP.D.GKL...S.NYA...S.NPETKKT..KLP.GS...ISSANR | |
| Retrocopy | AQLNTGNAFPVGTRPEGMIMCCVVEKPRDHGKLTQRSENYAMLLSYNPETKKTHAKLPLGSTMLISSANR |
| Parental | AVVGVVAGGGRIDKPILKAGRAYHKYKAKRNCWPRVRGVAMNPVEHPFGGGNHQHIGKPSTIRRDAPAG |
| .VVGVVAGG...DKPILKAG.AYHKYKAKRN.WPRV.G...NPVE....GGNHQHI.KP.TI.RDA..G | |
| Retrocopy | VVVGVVAGGD*TDKPILKAGWAYHKYKAKRNFWPRVWGANTNPVELRVRGGNHQHISKPFTICRDASTG |
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 | 122 .23 RPM |
| SRP051959_heart | 0 .00 RPM | 100 .28 RPM |
| SRP051959_kidney | 0 .00 RPM | 110 .71 RPM |
| SRP051959_liver | 0 .00 RPM | 130 .35 RPM |
| SRP051959_lung | 0 .00 RPM | 129 .60 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 246 .09 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 140 .83 RPM |
| SRP051959_spleen | 0 .00 RPM | 167 .08 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2047 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2047 was not experimentally validated.