RetrogeneDB ID: | retro_cjac_3226 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 9:64031590..64032100(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000023388 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TESC | ||
| Ensembl ID: | ENSCJAG00000009509 | ||
| Aliases: | None | ||
| Description: | tescalcin [Source:HGNC Symbol;Acc:26065] |
Retrocopy-Parental alignment summary:
>retro_cjac_3226
AAGGAGAACTTCAACAATGTCCCGGACCTGGAGCTCAACCCCATCCGTTCCAAAATTGTTCGTGCCTTCTTCGACCACAG
GAACCTGCGCAAGGGACCCAGCGGCCTGGCTGATGAGATCAATTTCGAGGACTTCCTGACTATCATGTCCTACTTCCGGC
CCATCGACACCAACACGGGCGAGGAGCAGGTGGCGCAGTCCCGGAAGGAGAAGCTGAGATTTCTGTTCCACATGTATGAC
GCCGACAGCGACGGCCGCATCACCCTGGAAGAATACCGAAATGTGGTCGAGGAGCTGCTGTTGGAAAACCAGCACATGGA
GGAGTCCGCTGGCTCCATCGCCGAGGGGGCCATGATGGAGGCGGCCAGCGTGTGCTTGGGGCAAATGGAGCCTGATCAGG
TGTACGAAGGGATCACCTTCGAGGACTTCCTGAAGATCTTGCAGGGGATCGACATTGAGTCCAAGATGCACATCTGCTTC
CTTAACATGGAAACCATGGCCCTCTGCCAC
ORF - retro_cjac_3226 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 89.47 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | KENFNNVPDLELNPIRSKIVRAFFDNRNLRKGPSGLADEINFEDFLTIMSYFRPIDTTMGEEQVELSRKE |
| KENFNNVPDLELNPIRSKIVRAFFD.RNLRKGPSGLADEINFEDFLTIMSYFRPIDT..GEEQV..SRKE | |
| Retrocopy | KENFNNVPDLELNPIRSKIVRAFFDHRNLRKGPSGLADEINFEDFLTIMSYFRPIDTNTGEEQVAQSRKE |
| Parental | KLRFLFHMYDSDSDGRITLEEYRNVVEELLSGNPHIEKESARSIADGAMMEAASVCVGQMEPDQVYEGIT |
| KLRFLFHMYD.DSDGRITLEEYRNVVEELL..N.H.E.ESA.SIA.GAMMEAASVC.GQMEPDQVYEGIT | |
| Retrocopy | KLRFLFHMYDADSDGRITLEEYRNVVEELLLENQHME-ESAGSIAEGAMMEAASVCLGQMEPDQVYEGIT |
| Parental | FEDFLKIWQGIDIETKMHVRFLNMETMALCH |
| FEDFLKI.QGIDIE.KMH..FLNMETMALCH | |
| Retrocopy | FEDFLKILQGIDIESKMHICFLNMETMALCH |
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 .04 RPM | 0 .78 RPM |
| SRP051959_heart | 0 .28 RPM | 5 .77 RPM |
| SRP051959_kidney | 0 .04 RPM | 0 .64 RPM |
| SRP051959_liver | 0 .09 RPM | 0 .35 RPM |
| SRP051959_lung | 0 .13 RPM | 0 .78 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 0 .27 RPM |
| SRP051959_skeletal_muscle | 0 .02 RPM | 0 .59 RPM |
| SRP051959_spleen | 0 .04 RPM | 1 .60 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3226 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3226 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_3226 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 | ENSCJAG00000009509 | 1 retrocopy |
retro_cjac_3226 ,
|
| Mus musculus | ENSMUSG00000029359 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000001128 | 1 retrocopy |